diff --git a/.env.example b/.env.example
index 59b93dd1b..40204aeae 100644
--- a/.env.example
+++ b/.env.example
@@ -32,3 +32,6 @@ INFOQUEST_API_KEY=your-infoquest-api-key
 
 # GitHub API Token
 # GITHUB_TOKEN=your-github-token
+
+# Database (only needed when config.yaml has database.backend: postgres)
+# DATABASE_URL=postgresql://deerflow:password@localhost:5432/deerflow
diff --git a/backend/app/gateway/deps.py b/backend/app/gateway/deps.py
index 115868331..69ce86d9e 100644
--- a/backend/app/gateway/deps.py
+++ b/backend/app/gateway/deps.py
@@ -14,6 +14,7 @@ from contextlib import AsyncExitStack, asynccontextmanager
 from fastapi import FastAPI, HTTPException, Request
 
 from deerflow.runtime import RunManager, StreamBridge
+from deerflow.runtime.runs.store.base import RunStore
 
 
 @asynccontextmanager
@@ -26,18 +27,33 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
             yield
     """
     from deerflow.agents.checkpointer.async_provider import make_checkpointer
+    from deerflow.config import get_app_config
+    from deerflow.persistence.engine import close_engine, init_engine_from_config
     from deerflow.runtime import make_store, make_stream_bridge
+    from deerflow.runtime.runs.store.memory import MemoryRunStore
 
     async with AsyncExitStack() as stack:
         app.state.stream_bridge = await stack.enter_async_context(make_stream_bridge())
         app.state.checkpointer = await stack.enter_async_context(make_checkpointer())
         app.state.store = await stack.enter_async_context(make_store())
         app.state.run_manager = RunManager()
-        yield
+
+        # Initialize persistence layer from unified database config
+        config = get_app_config()
+        await init_engine_from_config(config.database)
+
+        # Initialize run store (MemoryRunStore for now; switch to ORM-backed
+        # RunRepository when models are implemented)
+        app.state.run_store = MemoryRunStore()
+
+        try:
+            yield
+        finally:
+            await close_engine()
 
 
 # ---------------------------------------------------------------------------
-# Getters – called by routers per-request
+# Getters -- called by routers per-request
 # ---------------------------------------------------------------------------
 
 
@@ -68,3 +84,20 @@ def get_checkpointer(request: Request):
 def get_store(request: Request):
     """Return the global store (may be ``None`` if not configured)."""
     return getattr(request.app.state, "store", None)
+
+
+def get_run_store(request: Request) -> RunStore:
+    """Return the RunStore, or 503 if not available."""
+    store = getattr(request.app.state, "run_store", None)
+    if store is None:
+        raise HTTPException(status_code=503, detail="Run store not available")
+    return store
+
+
+async def get_current_user(request: Request) -> str | None:
+    """Extract user identity from request.
+
+    Phase 2: always returns None (no authentication).
+    Phase 3: extract user_id from JWT / session / API key header.
+    """
+    return None
diff --git a/backend/packages/harness/deerflow/agents/checkpointer/async_provider.py b/backend/packages/harness/deerflow/agents/checkpointer/async_provider.py
index 9380d781e..46e0e094d 100644
--- a/backend/packages/harness/deerflow/agents/checkpointer/async_provider.py
+++ b/backend/packages/harness/deerflow/agents/checkpointer/async_provider.py
@@ -83,23 +83,76 @@ async def _async_checkpointer(config) -> AsyncIterator[Checkpointer]:
 
 
 @contextlib.asynccontextmanager
-async def make_checkpointer() -> AsyncIterator[Checkpointer]:
-    """Async context manager that yields a checkpointer for the caller's lifetime.
-    Resources are opened on enter and closed on exit — no global state::
-
-        async with make_checkpointer() as checkpointer:
-            app.state.checkpointer = checkpointer
-
-    Yields an ``InMemorySaver`` when no checkpointer is configured in *config.yaml*.
-    """
-
-    config = get_app_config()
-
-    if config.checkpointer is None:
+async def _async_checkpointer_from_database(db_config) -> AsyncIterator[Checkpointer]:
+    """Async context manager that constructs a checkpointer from unified DatabaseConfig."""
+    if db_config.backend == "memory":
         from langgraph.checkpoint.memory import InMemorySaver
 
         yield InMemorySaver()
         return
 
-    async with _async_checkpointer(config.checkpointer) as saver:
-        yield saver
+    if db_config.backend == "sqlite":
+        try:
+            from langgraph.checkpoint.sqlite.aio import AsyncSqliteSaver
+        except ImportError as exc:
+            raise ImportError(SQLITE_INSTALL) from exc
+
+        conn_str = db_config.checkpointer_sqlite_path
+        ensure_sqlite_parent_dir(conn_str)
+        async with AsyncSqliteSaver.from_conn_string(conn_str) as saver:
+            await saver.setup()
+            yield saver
+        return
+
+    if db_config.backend == "postgres":
+        try:
+            from langgraph.checkpoint.postgres.aio import AsyncPostgresSaver
+        except ImportError as exc:
+            raise ImportError(POSTGRES_INSTALL) from exc
+
+        if not db_config.postgres_url:
+            raise ValueError("database.postgres_url is required for the postgres backend")
+
+        async with AsyncPostgresSaver.from_conn_string(db_config.postgres_url) as saver:
+            await saver.setup()
+            yield saver
+        return
+
+    raise ValueError(f"Unknown database backend: {db_config.backend!r}")
+
+
+@contextlib.asynccontextmanager
+async def make_checkpointer() -> AsyncIterator[Checkpointer]:
+    """Async context manager that yields a checkpointer for the caller's lifetime.
+    Resources are opened on enter and closed on exit -- no global state::
+
+        async with make_checkpointer() as checkpointer:
+            app.state.checkpointer = checkpointer
+
+    Yields an ``InMemorySaver`` when no checkpointer is configured in *config.yaml*.
+
+    Priority:
+    1. Legacy ``checkpointer:`` config section (backward compatible)
+    2. Unified ``database:`` config section
+    3. Default InMemorySaver
+    """
+
+    config = get_app_config()
+
+    # Legacy: standalone checkpointer config takes precedence
+    if config.checkpointer is not None:
+        async with _async_checkpointer(config.checkpointer) as saver:
+            yield saver
+            return
+
+    # Unified database config
+    db_config = getattr(config, "database", None)
+    if db_config is not None and db_config.backend != "memory":
+        async with _async_checkpointer_from_database(db_config) as saver:
+            yield saver
+            return
+
+    # Default: in-memory
+    from langgraph.checkpoint.memory import InMemorySaver
+
+    yield InMemorySaver()
diff --git a/backend/packages/harness/deerflow/config/app_config.py b/backend/packages/harness/deerflow/config/app_config.py
index d034ffc4c..85fbc51b7 100644
--- a/backend/packages/harness/deerflow/config/app_config.py
+++ b/backend/packages/harness/deerflow/config/app_config.py
@@ -9,6 +9,7 @@ from pydantic import BaseModel, ConfigDict, Field
 
 from deerflow.config.acp_config import load_acp_config_from_dict
 from deerflow.config.checkpointer_config import CheckpointerConfig, load_checkpointer_config_from_dict
+from deerflow.config.database_config import DatabaseConfig
 from deerflow.config.extensions_config import ExtensionsConfig
 from deerflow.config.guardrails_config import load_guardrails_config_from_dict
 from deerflow.config.memory_config import load_memory_config_from_dict
@@ -41,6 +42,7 @@ class AppConfig(BaseModel):
     extensions: ExtensionsConfig = Field(default_factory=ExtensionsConfig, description="Extensions configuration (MCP servers and skills state)")
     tool_search: ToolSearchConfig = Field(default_factory=ToolSearchConfig, description="Tool search / deferred loading configuration")
     model_config = ConfigDict(extra="allow", frozen=False)
+    database: DatabaseConfig = Field(default_factory=DatabaseConfig, description="Unified database backend configuration")
     checkpointer: CheckpointerConfig | None = Field(default=None, description="Checkpointer configuration")
     stream_bridge: StreamBridgeConfig | None = Field(default=None, description="Stream bridge configuration")
 
diff --git a/backend/packages/harness/deerflow/config/database_config.py b/backend/packages/harness/deerflow/config/database_config.py
new file mode 100644
index 000000000..b201f725c
--- /dev/null
+++ b/backend/packages/harness/deerflow/config/database_config.py
@@ -0,0 +1,85 @@
+"""Unified database backend configuration.
+
+Controls BOTH the LangGraph checkpointer and the DeerFlow application
+persistence layer (runs, threads metadata, users, etc.). The user
+configures one backend; the system handles physical separation details.
+
+SQLite mode: checkpointer and app use different .db files in the same
+directory to avoid write-lock contention. This is automatic.
+
+Postgres mode: both use the same database URL but maintain independent
+connection pools with different lifecycles.
+
+Memory mode: checkpointer uses MemorySaver, app uses in-memory stores.
+No database is initialized.
+
+Sensitive values (postgres_url) should use $VAR syntax in config.yaml
+to reference environment variables from .env:
+
+    database:
+      backend: postgres
+      postgres_url: $DATABASE_URL
+
+The $VAR resolution is handled by AppConfig.resolve_env_variables()
+before this config is instantiated -- DatabaseConfig itself does not
+need to do any environment variable processing.
+"""
+
+from __future__ import annotations
+
+import os
+from typing import Literal
+
+from pydantic import BaseModel, Field
+
+
+class DatabaseConfig(BaseModel):
+    backend: Literal["memory", "sqlite", "postgres"] = Field(
+        default="memory",
+        description=("Storage backend for both checkpointer and application data. 'memory' for development (no persistence across restarts), 'sqlite' for single-node deployment, 'postgres' for production multi-node deployment."),
+    )
+    sqlite_dir: str = Field(
+        default="./data",
+        description=("Directory for SQLite database files. Checkpointer uses {sqlite_dir}/checkpoints.db, application data uses {sqlite_dir}/app.db."),
+    )
+    postgres_url: str = Field(
+        default="",
+        description=(
+            "PostgreSQL connection URL, shared by checkpointer and app. "
+            "Use $DATABASE_URL in config.yaml to reference .env. "
+            "Example: postgresql://user:pass@host:5432/deerflow "
+            "(the +asyncpg driver suffix is added automatically where needed)."
+        ),
+    )
+    echo_sql: bool = Field(
+        default=False,
+        description="Echo all SQL statements to log (debug only).",
+    )
+    pool_size: int = Field(
+        default=5,
+        description="Connection pool size for the app ORM engine (postgres only).",
+    )
+
+    # -- Derived helpers (not user-configured) --
+
+    @property
+    def checkpointer_sqlite_path(self) -> str:
+        """SQLite file path for the LangGraph checkpointer."""
+        return os.path.join(self.sqlite_dir, "checkpoints.db")
+
+    @property
+    def app_sqlite_path(self) -> str:
+        """SQLite file path for application ORM data."""
+        return os.path.join(self.sqlite_dir, "app.db")
+
+    @property
+    def app_sqlalchemy_url(self) -> str:
+        """SQLAlchemy async URL for the application ORM engine."""
+        if self.backend == "sqlite":
+            return f"sqlite+aiosqlite:///{self.app_sqlite_path}"
+        if self.backend == "postgres":
+            url = self.postgres_url
+            if url.startswith("postgresql://"):
+                url = url.replace("postgresql://", "postgresql+asyncpg://", 1)
+            return url
+        raise ValueError(f"No SQLAlchemy URL for backend={self.backend!r}")
diff --git a/backend/packages/harness/deerflow/persistence/__init__.py b/backend/packages/harness/deerflow/persistence/__init__.py
new file mode 100644
index 000000000..dfd64be95
--- /dev/null
+++ b/backend/packages/harness/deerflow/persistence/__init__.py
@@ -0,0 +1,13 @@
+"""DeerFlow application persistence layer (SQLAlchemy 2.0 async ORM).
+
+This module manages DeerFlow's own application data -- runs metadata,
+thread ownership, cron jobs, users. It is completely separate from
+LangGraph's checkpointer, which manages graph execution state.
+
+Usage:
+    from deerflow.persistence import init_engine, close_engine, get_session_factory
+"""
+
+from deerflow.persistence.engine import close_engine, get_engine, get_session_factory, init_engine
+
+__all__ = ["close_engine", "get_engine", "get_session_factory", "init_engine"]
diff --git a/backend/packages/harness/deerflow/persistence/base.py b/backend/packages/harness/deerflow/persistence/base.py
new file mode 100644
index 000000000..fd99d5f74
--- /dev/null
+++ b/backend/packages/harness/deerflow/persistence/base.py
@@ -0,0 +1,40 @@
+"""SQLAlchemy declarative base with automatic to_dict support.
+
+All DeerFlow ORM models inherit from this Base. It provides a generic
+to_dict() method via SQLAlchemy's inspect() so individual models don't
+need to write their own serialization logic.
+
+LangGraph's checkpointer tables are NOT managed by this Base.
+"""
+
+from __future__ import annotations
+
+from sqlalchemy import inspect as sa_inspect
+from sqlalchemy.orm import DeclarativeBase
+
+
+class Base(DeclarativeBase):
+    """Base class for all DeerFlow ORM models.
+
+    Provides:
+    - Automatic to_dict() via SQLAlchemy column inspection.
+    - Standard __repr__() showing all column values.
+    """
+
+    def to_dict(self, *, exclude: set[str] | None = None) -> dict:
+        """Convert ORM instance to plain dict.
+
+        Uses SQLAlchemy's inspect() to iterate mapped column attributes.
+
+        Args:
+            exclude: Optional set of column keys to omit.
+
+        Returns:
+            Dict of {column_key: value} for all mapped columns.
+        """
+        exclude = exclude or set()
+        return {c.key: getattr(self, c.key) for c in sa_inspect(type(self)).mapper.column_attrs if c.key not in exclude}
+
+    def __repr__(self) -> str:
+        cols = ", ".join(f"{c.key}={getattr(self, c.key)!r}" for c in sa_inspect(type(self)).mapper.column_attrs)
+        return f"{type(self).__name__}({cols})"
diff --git a/backend/packages/harness/deerflow/persistence/engine.py b/backend/packages/harness/deerflow/persistence/engine.py
new file mode 100644
index 000000000..82bce2a5b
--- /dev/null
+++ b/backend/packages/harness/deerflow/persistence/engine.py
@@ -0,0 +1,116 @@
+"""Async SQLAlchemy engine lifecycle management.
+
+Initializes at Gateway startup, provides session factory for
+repositories, disposes at shutdown.
+
+When database.backend="memory", init_engine is a no-op and
+get_session_factory() returns None. Repositories must check for
+None and fall back to in-memory implementations.
+"""
+
+from __future__ import annotations
+
+import logging
+
+from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker, create_async_engine
+
+logger = logging.getLogger(__name__)
+
+_engine: AsyncEngine | None = None
+_session_factory: async_sessionmaker[AsyncSession] | None = None
+
+
+async def init_engine(
+    backend: str,
+    *,
+    url: str = "",
+    echo: bool = False,
+    pool_size: int = 5,
+    sqlite_dir: str = "",
+) -> None:
+    """Create the async engine and session factory, then auto-create tables.
+
+    Args:
+        backend: "memory", "sqlite", or "postgres".
+        url: SQLAlchemy async URL (for sqlite/postgres).
+        echo: Echo SQL to log.
+        pool_size: Postgres connection pool size.
+        sqlite_dir: Directory to create for SQLite (ensured to exist).
+    """
+    global _engine, _session_factory
+
+    if backend == "memory":
+        logger.info("Persistence backend=memory -- ORM engine not initialized")
+        return
+
+    if backend == "postgres":
+        try:
+            import asyncpg  # noqa: F401
+        except ImportError:
+            raise ImportError("database.backend is set to 'postgres' but asyncpg is not installed.\nInstall it with:\n    uv sync --extra postgres\nOr switch to backend: sqlite in config.yaml for single-node deployment.") from None
+
+    if backend == "sqlite":
+        import os
+
+        os.makedirs(sqlite_dir or ".", exist_ok=True)
+        _engine = create_async_engine(url, echo=echo)
+    elif backend == "postgres":
+        _engine = create_async_engine(
+            url,
+            echo=echo,
+            pool_size=pool_size,
+            pool_pre_ping=True,
+        )
+    else:
+        raise ValueError(f"Unknown persistence backend: {backend!r}")
+
+    _session_factory = async_sessionmaker(_engine, expire_on_commit=False)
+
+    # Auto-create tables (dev convenience). Production should use Alembic.
+    from deerflow.persistence.base import Base
+
+    # Import all models so Base.metadata discovers them.
+    # When no models exist yet (scaffolding phase), this is a no-op.
+    try:
+        import deerflow.persistence.models  # noqa: F401
+    except ImportError:
+        pass
+
+    async with _engine.begin() as conn:
+        await conn.run_sync(Base.metadata.create_all)
+
+    logger.info("Persistence engine initialized: backend=%s", backend)
+
+
+async def init_engine_from_config(config) -> None:
+    """Convenience: init engine from a DatabaseConfig object."""
+    if config.backend == "memory":
+        await init_engine("memory")
+        return
+    await init_engine(
+        backend=config.backend,
+        url=config.app_sqlalchemy_url,
+        echo=config.echo_sql,
+        pool_size=config.pool_size,
+        sqlite_dir=config.sqlite_dir if config.backend == "sqlite" else "",
+    )
+
+
+def get_session_factory() -> async_sessionmaker[AsyncSession] | None:
+    """Return the async session factory, or None if backend=memory."""
+    return _session_factory
+
+
+def get_engine() -> AsyncEngine | None:
+    """Return the async engine, or None if not initialized."""
+    return _engine
+
+
+async def close_engine() -> None:
+    """Dispose the engine, release all connections."""
+    global _engine, _session_factory
+    if _engine is not None:
+        await _engine.dispose()
+        logger.info("Persistence engine closed")
+    _engine = None
+    _session_factory = None
diff --git a/backend/packages/harness/deerflow/persistence/migrations/alembic.ini b/backend/packages/harness/deerflow/persistence/migrations/alembic.ini
new file mode 100644
index 000000000..adeccef32
--- /dev/null
+++ b/backend/packages/harness/deerflow/persistence/migrations/alembic.ini
@@ -0,0 +1,38 @@
+[alembic]
+script_location = %(here)s
+# Default URL for offline mode / autogenerate.
+# Runtime uses engine from DeerFlow config.
+sqlalchemy.url = sqlite+aiosqlite:///./data/app.db
+
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S
diff --git a/backend/packages/harness/deerflow/persistence/migrations/env.py b/backend/packages/harness/deerflow/persistence/migrations/env.py
new file mode 100644
index 000000000..45bd985ef
--- /dev/null
+++ b/backend/packages/harness/deerflow/persistence/migrations/env.py
@@ -0,0 +1,63 @@
+"""Alembic environment for DeerFlow application tables.
+
+ONLY manages DeerFlow's tables (runs, threads_meta, cron_jobs, users).
+LangGraph's checkpointer tables are managed by LangGraph itself -- they
+have their own schema lifecycle and must not be touched by Alembic.
+"""
+
+from __future__ import annotations
+
+import asyncio
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy.ext.asyncio import create_async_engine
+
+from deerflow.persistence.base import Base
+
+# Import all models so metadata is populated.
+try:
+    import deerflow.persistence.models  # noqa: F401
+except ImportError:
+    pass
+
+config = context.config
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+target_metadata = Base.metadata
+
+
+def run_migrations_offline() -> None:
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        render_as_batch=True,
+    )
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def do_run_migrations(connection):
+    context.configure(
+        connection=connection,
+        target_metadata=target_metadata,
+        render_as_batch=True,  # Required for SQLite ALTER TABLE support
+    )
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_migrations_online() -> None:
+    connectable = create_async_engine(config.get_main_option("sqlalchemy.url"))
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
+    await connectable.dispose()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    asyncio.run(run_migrations_online())
diff --git a/backend/packages/harness/deerflow/persistence/migrations/versions/.gitkeep b/backend/packages/harness/deerflow/persistence/migrations/versions/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/backend/packages/harness/deerflow/runtime/runs/store/__init__.py b/backend/packages/harness/deerflow/runtime/runs/store/__init__.py
new file mode 100644
index 000000000..265a6fffb
--- /dev/null
+++ b/backend/packages/harness/deerflow/runtime/runs/store/__init__.py
@@ -0,0 +1,4 @@
+from deerflow.runtime.runs.store.base import RunStore
+from deerflow.runtime.runs.store.memory import MemoryRunStore
+
+__all__ = ["MemoryRunStore", "RunStore"]
diff --git a/backend/packages/harness/deerflow/runtime/runs/store/base.py b/backend/packages/harness/deerflow/runtime/runs/store/base.py
new file mode 100644
index 000000000..993db21b4
--- /dev/null
+++ b/backend/packages/harness/deerflow/runtime/runs/store/base.py
@@ -0,0 +1,59 @@
+"""Abstract interface for run metadata storage.
+
+RunManager depends on this interface. Implementations:
+- MemoryRunStore: in-memory dict (development, tests)
+- Future: RunRepository backed by SQLAlchemy ORM
+
+All methods accept an optional owner_id for user isolation.
+When owner_id is None, no user filtering is applied (single-user mode).
+"""
+
+from __future__ import annotations
+
+import abc
+from typing import Any
+
+
+class RunStore(abc.ABC):
+    @abc.abstractmethod
+    async def put(
+        self,
+        run_id: str,
+        *,
+        thread_id: str,
+        assistant_id: str | None = None,
+        owner_id: str | None = None,
+        status: str = "pending",
+        multitask_strategy: str = "reject",
+        metadata: dict[str, Any] | None = None,
+        kwargs: dict[str, Any] | None = None,
+        error: str | None = None,
+        created_at: str | None = None,
+    ) -> None: ...
+
+    @abc.abstractmethod
+    async def get(self, run_id: str) -> dict[str, Any] | None: ...
+
+    @abc.abstractmethod
+    async def list_by_thread(
+        self,
+        thread_id: str,
+        *,
+        owner_id: str | None = None,
+        limit: int = 100,
+    ) -> list[dict[str, Any]]: ...
+
+    @abc.abstractmethod
+    async def update_status(
+        self,
+        run_id: str,
+        status: str,
+        *,
+        error: str | None = None,
+    ) -> None: ...
+
+    @abc.abstractmethod
+    async def delete(self, run_id: str) -> None: ...
+
+    @abc.abstractmethod
+    async def list_pending(self, *, before: str | None = None) -> list[dict[str, Any]]: ...
diff --git a/backend/packages/harness/deerflow/runtime/runs/store/memory.py b/backend/packages/harness/deerflow/runtime/runs/store/memory.py
new file mode 100644
index 000000000..a7a22e4c1
--- /dev/null
+++ b/backend/packages/harness/deerflow/runtime/runs/store/memory.py
@@ -0,0 +1,69 @@
+"""In-memory RunStore. Used when database.backend=memory (default) and in tests.
+
+Equivalent to the original RunManager._runs dict behavior.
+"""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+from typing import Any
+
+from deerflow.runtime.runs.store.base import RunStore
+
+
+class MemoryRunStore(RunStore):
+    def __init__(self) -> None:
+        self._runs: dict[str, dict[str, Any]] = {}
+
+    async def put(
+        self,
+        run_id,
+        *,
+        thread_id,
+        assistant_id=None,
+        owner_id=None,
+        status="pending",
+        multitask_strategy="reject",
+        metadata=None,
+        kwargs=None,
+        error=None,
+        created_at=None,
+    ):
+        now = datetime.now(UTC).isoformat()
+        self._runs[run_id] = {
+            "run_id": run_id,
+            "thread_id": thread_id,
+            "assistant_id": assistant_id,
+            "owner_id": owner_id,
+            "status": status,
+            "multitask_strategy": multitask_strategy,
+            "metadata": metadata or {},
+            "kwargs": kwargs or {},
+            "error": error,
+            "created_at": created_at or now,
+            "updated_at": now,
+        }
+
+    async def get(self, run_id):
+        return self._runs.get(run_id)
+
+    async def list_by_thread(self, thread_id, *, owner_id=None, limit=100):
+        results = [r for r in self._runs.values() if r["thread_id"] == thread_id and (owner_id is None or r.get("owner_id") == owner_id)]
+        results.sort(key=lambda r: r["created_at"], reverse=True)
+        return results[:limit]
+
+    async def update_status(self, run_id, status, *, error=None):
+        if run_id in self._runs:
+            self._runs[run_id]["status"] = status
+            if error is not None:
+                self._runs[run_id]["error"] = error
+            self._runs[run_id]["updated_at"] = datetime.now(UTC).isoformat()
+
+    async def delete(self, run_id):
+        self._runs.pop(run_id, None)
+
+    async def list_pending(self, *, before=None):
+        now = before or datetime.now(UTC).isoformat()
+        results = [r for r in self._runs.values() if r["status"] == "pending" and r["created_at"] <= now]
+        results.sort(key=lambda r: r["created_at"])
+        return results
diff --git a/backend/packages/harness/pyproject.toml b/backend/packages/harness/pyproject.toml
index 9315d883a..f7b80081c 100644
--- a/backend/packages/harness/pyproject.toml
+++ b/backend/packages/harness/pyproject.toml
@@ -31,6 +31,14 @@ dependencies = [
     "langchain-google-genai>=4.2.1",
     "langgraph-checkpoint-sqlite>=3.0.3",
     "langgraph-sdk>=0.1.51",
+    "sqlalchemy[asyncio]>=2.0,<3.0",
+    "aiosqlite>=0.19",
+    "alembic>=1.13",
+]
+
+[project.optional-dependencies]
+postgres = [
+    "asyncpg>=0.29",
 ]
 
 [build-system]
diff --git a/backend/tests/test_persistence_scaffold.py b/backend/tests/test_persistence_scaffold.py
new file mode 100644
index 000000000..e45389ba9
--- /dev/null
+++ b/backend/tests/test_persistence_scaffold.py
@@ -0,0 +1,231 @@
+"""Tests for the persistence layer scaffolding.
+
+Tests:
+1. DatabaseConfig property derivation (paths, URLs)
+2. MemoryRunStore CRUD + owner_id filtering
+3. Base.to_dict() via inspect mixin
+4. Engine init/close lifecycle (memory + SQLite)
+5. Postgres missing-dep error message
+"""
+
+from datetime import UTC, datetime
+
+import pytest
+
+from deerflow.config.database_config import DatabaseConfig
+from deerflow.runtime.runs.store.memory import MemoryRunStore
+
+
+# -- DatabaseConfig --
+
+
+class TestDatabaseConfig:
+    def test_defaults(self):
+        c = DatabaseConfig()
+        assert c.backend == "memory"
+        assert c.pool_size == 5
+
+    def test_sqlite_paths_are_different(self):
+        c = DatabaseConfig(backend="sqlite", sqlite_dir="./mydata")
+        assert c.checkpointer_sqlite_path.endswith("checkpoints.db")
+        assert c.app_sqlite_path.endswith("app.db")
+        assert "mydata" in c.checkpointer_sqlite_path
+        assert c.checkpointer_sqlite_path != c.app_sqlite_path
+
+    def test_app_sqlalchemy_url_sqlite(self):
+        c = DatabaseConfig(backend="sqlite", sqlite_dir="./data")
+        url = c.app_sqlalchemy_url
+        assert url.startswith("sqlite+aiosqlite:///")
+        assert "app.db" in url
+
+    def test_app_sqlalchemy_url_postgres(self):
+        c = DatabaseConfig(
+            backend="postgres",
+            postgres_url="postgresql://u:p@h:5432/db",
+        )
+        url = c.app_sqlalchemy_url
+        assert url.startswith("postgresql+asyncpg://")
+        assert "u:p@h:5432/db" in url
+
+    def test_app_sqlalchemy_url_postgres_already_asyncpg(self):
+        c = DatabaseConfig(
+            backend="postgres",
+            postgres_url="postgresql+asyncpg://u:p@h:5432/db",
+        )
+        url = c.app_sqlalchemy_url
+        assert url.count("asyncpg") == 1
+
+    def test_memory_has_no_url(self):
+        c = DatabaseConfig(backend="memory")
+        with pytest.raises(ValueError, match="No SQLAlchemy URL"):
+            _ = c.app_sqlalchemy_url
+
+
+# -- MemoryRunStore --
+
+
+class TestMemoryRunStore:
+    @pytest.fixture
+    def store(self):
+        return MemoryRunStore()
+
+    @pytest.mark.anyio
+    async def test_put_and_get(self, store):
+        await store.put("r1", thread_id="t1", status="pending")
+        row = await store.get("r1")
+        assert row is not None
+        assert row["run_id"] == "r1"
+        assert row["status"] == "pending"
+
+    @pytest.mark.anyio
+    async def test_get_missing_returns_none(self, store):
+        assert await store.get("nope") is None
+
+    @pytest.mark.anyio
+    async def test_update_status(self, store):
+        await store.put("r1", thread_id="t1")
+        await store.update_status("r1", "running")
+        assert (await store.get("r1"))["status"] == "running"
+
+    @pytest.mark.anyio
+    async def test_update_status_with_error(self, store):
+        await store.put("r1", thread_id="t1")
+        await store.update_status("r1", "error", error="boom")
+        row = await store.get("r1")
+        assert row["status"] == "error"
+        assert row["error"] == "boom"
+
+    @pytest.mark.anyio
+    async def test_list_by_thread(self, store):
+        await store.put("r1", thread_id="t1")
+        await store.put("r2", thread_id="t1")
+        await store.put("r3", thread_id="t2")
+        rows = await store.list_by_thread("t1")
+        assert len(rows) == 2
+        assert all(r["thread_id"] == "t1" for r in rows)
+
+    @pytest.mark.anyio
+    async def test_list_by_thread_owner_filter(self, store):
+        await store.put("r1", thread_id="t1", owner_id="alice")
+        await store.put("r2", thread_id="t1", owner_id="bob")
+        rows = await store.list_by_thread("t1", owner_id="alice")
+        assert len(rows) == 1
+        assert rows[0]["owner_id"] == "alice"
+
+    @pytest.mark.anyio
+    async def test_owner_none_returns_all(self, store):
+        await store.put("r1", thread_id="t1", owner_id="alice")
+        await store.put("r2", thread_id="t1", owner_id="bob")
+        rows = await store.list_by_thread("t1", owner_id=None)
+        assert len(rows) == 2
+
+    @pytest.mark.anyio
+    async def test_delete(self, store):
+        await store.put("r1", thread_id="t1")
+        await store.delete("r1")
+        assert await store.get("r1") is None
+
+    @pytest.mark.anyio
+    async def test_delete_nonexistent_is_noop(self, store):
+        await store.delete("nope")  # should not raise
+
+    @pytest.mark.anyio
+    async def test_list_pending(self, store):
+        await store.put("r1", thread_id="t1", status="pending")
+        await store.put("r2", thread_id="t1", status="running")
+        await store.put("r3", thread_id="t2", status="pending")
+        pending = await store.list_pending()
+        assert len(pending) == 2
+        assert all(r["status"] == "pending" for r in pending)
+
+    @pytest.mark.anyio
+    async def test_list_pending_respects_before(self, store):
+        past = "2020-01-01T00:00:00+00:00"
+        future = "2099-01-01T00:00:00+00:00"
+        await store.put("r1", thread_id="t1", status="pending", created_at=past)
+        await store.put("r2", thread_id="t1", status="pending", created_at=future)
+        pending = await store.list_pending(before=datetime.now(UTC).isoformat())
+        assert len(pending) == 1
+        assert pending[0]["run_id"] == "r1"
+
+    @pytest.mark.anyio
+    async def test_list_pending_fifo_order(self, store):
+        await store.put("r2", thread_id="t1", status="pending", created_at="2024-01-02T00:00:00+00:00")
+        await store.put("r1", thread_id="t1", status="pending", created_at="2024-01-01T00:00:00+00:00")
+        pending = await store.list_pending()
+        assert pending[0]["run_id"] == "r1"
+
+
+# -- Base.to_dict mixin --
+
+
+class TestBaseToDictMixin:
+    @pytest.mark.anyio
+    async def test_to_dict_and_exclude(self, tmp_path):
+        """Create a temp SQLite DB with a minimal model, verify to_dict."""
+        from sqlalchemy import String
+        from sqlalchemy.ext.asyncio import async_sessionmaker, create_async_engine
+        from sqlalchemy.orm import Mapped, mapped_column
+
+        from deerflow.persistence.base import Base
+
+        class _Tmp(Base):
+            __tablename__ = "_tmp_test"
+            id: Mapped[str] = mapped_column(String(64), primary_key=True)
+            name: Mapped[str] = mapped_column(String(128))
+
+        engine = create_async_engine(f"sqlite+aiosqlite:///{tmp_path / 'test.db'}")
+        async with engine.begin() as conn:
+            await conn.run_sync(Base.metadata.create_all)
+
+        sf = async_sessionmaker(engine, expire_on_commit=False)
+        async with sf() as session:
+            session.add(_Tmp(id="1", name="hello"))
+            await session.commit()
+            obj = await session.get(_Tmp, "1")
+
+            assert obj.to_dict() == {"id": "1", "name": "hello"}
+            assert obj.to_dict(exclude={"name"}) == {"id": "1"}
+            assert "_Tmp" in repr(obj)
+
+        await engine.dispose()
+
+
+# -- Engine lifecycle --
+
+
+class TestEngineLifecycle:
+    @pytest.mark.anyio
+    async def test_memory_is_noop(self):
+        from deerflow.persistence.engine import close_engine, get_session_factory, init_engine
+
+        await init_engine("memory")
+        assert get_session_factory() is None
+        await close_engine()
+
+    @pytest.mark.anyio
+    async def test_sqlite_creates_engine(self, tmp_path):
+        from deerflow.persistence.engine import close_engine, get_session_factory, init_engine
+
+        url = f"sqlite+aiosqlite:///{tmp_path / 'test.db'}"
+        await init_engine("sqlite", url=url, sqlite_dir=str(tmp_path))
+        sf = get_session_factory()
+        assert sf is not None
+        async with sf() as session:
+            assert session is not None
+        await close_engine()
+        assert get_session_factory() is None
+
+    @pytest.mark.anyio
+    async def test_postgres_without_asyncpg_gives_actionable_error(self):
+        """If asyncpg is not installed, error message tells user what to do."""
+        from deerflow.persistence.engine import init_engine
+
+        try:
+            import asyncpg  # noqa: F401
+
+            pytest.skip("asyncpg is installed -- cannot test missing-dep path")
+        except ImportError:
+            pass
+        with pytest.raises(ImportError, match="uv sync --extra postgres"):
+            await init_engine("postgres", url="postgresql+asyncpg://x:x@localhost/x")
diff --git a/backend/uv.lock b/backend/uv.lock
index af1aab013..67d6cf852 100644
--- a/backend/uv.lock
+++ b/backend/uv.lock
@@ -158,6 +158,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/00/b7/e3bf5133d697a08128598c8d0abc5e16377b51465a33756de24fa7dee953/aiosqlite-0.22.1-py3-none-any.whl", hash = "sha256:21c002eb13823fad740196c5a2e9d8e62f6243bd9e7e4a1f87fb5e44ecb4fceb", size = 17405, upload-time = "2025-12-23T19:25:42.139Z" },
 ]
 
+[[package]]
+name = "alembic"
+version = "1.18.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "mako" },
+    { name = "sqlalchemy" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/94/13/8b084e0f2efb0275a1d534838844926f798bd766566b1375174e2448cd31/alembic-1.18.4.tar.gz", hash = "sha256:cb6e1fd84b6174ab8dbb2329f86d631ba9559dd78df550b57804d607672cedbc", size = 2056725, upload-time = "2026-02-10T16:00:47.195Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/d2/29/6533c317b74f707ea28f8d633734dbda2119bbadfc61b2f3640ba835d0f7/alembic-1.18.4-py3-none-any.whl", hash = "sha256:a5ed4adcf6d8a4cb575f3d759f071b03cd6e5c7618eb796cb52497be25bfe19a", size = 263893, upload-time = "2026-02-10T16:00:49.997Z" },
+]
+
 [[package]]
 name = "annotated-doc"
 version = "0.0.4"
@@ -208,6 +222,46 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/38/0e/27be9fdef66e72d64c0cdc3cc2823101b80585f8119b5c112c2e8f5f7dab/anyio-4.12.1-py3-none-any.whl", hash = "sha256:d405828884fc140aa80a3c667b8beed277f1dfedec42ba031bd6ac3db606ab6c", size = 113592, upload-time = "2026-01-06T11:45:19.497Z" },
 ]
 
+[[package]]
+name = "asyncpg"
+version = "0.31.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/fe/cc/d18065ce2380d80b1bcce927c24a2642efd38918e33fd724bc4bca904877/asyncpg-0.31.0.tar.gz", hash = "sha256:c989386c83940bfbd787180f2b1519415e2d3d6277a70d9d0f0145ac73500735", size = 993667, upload-time = "2025-11-24T23:27:00.812Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2a/a6/59d0a146e61d20e18db7396583242e32e0f120693b67a8de43f1557033e2/asyncpg-0.31.0-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:b44c31e1efc1c15188ef183f287c728e2046abb1d26af4d20858215d50d91fad", size = 662042, upload-time = "2025-11-24T23:25:49.578Z" },
+    { url = "https://files.pythonhosted.org/packages/36/01/ffaa189dcb63a2471720615e60185c3f6327716fdc0fc04334436fbb7c65/asyncpg-0.31.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:0c89ccf741c067614c9b5fc7f1fc6f3b61ab05ae4aaa966e6fd6b93097c7d20d", size = 638504, upload-time = "2025-11-24T23:25:51.501Z" },
+    { url = "https://files.pythonhosted.org/packages/9f/62/3f699ba45d8bd24c5d65392190d19656d74ff0185f42e19d0bbd973bb371/asyncpg-0.31.0-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:12b3b2e39dc5470abd5e98c8d3373e4b1d1234d9fbdedf538798b2c13c64460a", size = 3426241, upload-time = "2025-11-24T23:25:53.278Z" },
+    { url = "https://files.pythonhosted.org/packages/8c/d1/a867c2150f9c6e7af6462637f613ba67f78a314b00db220cd26ff559d532/asyncpg-0.31.0-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:aad7a33913fb8bcb5454313377cc330fbb19a0cd5faa7272407d8a0c4257b671", size = 3520321, upload-time = "2025-11-24T23:25:54.982Z" },
+    { url = "https://files.pythonhosted.org/packages/7a/1a/cce4c3f246805ecd285a3591222a2611141f1669d002163abef999b60f98/asyncpg-0.31.0-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:3df118d94f46d85b2e434fd62c84cb66d5834d5a890725fe625f498e72e4d5ec", size = 3316685, upload-time = "2025-11-24T23:25:57.43Z" },
+    { url = "https://files.pythonhosted.org/packages/40/ae/0fc961179e78cc579e138fad6eb580448ecae64908f95b8cb8ee2f241f67/asyncpg-0.31.0-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:bd5b6efff3c17c3202d4b37189969acf8927438a238c6257f66be3c426beba20", size = 3471858, upload-time = "2025-11-24T23:25:59.636Z" },
+    { url = "https://files.pythonhosted.org/packages/52/b2/b20e09670be031afa4cbfabd645caece7f85ec62d69c312239de568e058e/asyncpg-0.31.0-cp312-cp312-win32.whl", hash = "sha256:027eaa61361ec735926566f995d959ade4796f6a49d3bde17e5134b9964f9ba8", size = 527852, upload-time = "2025-11-24T23:26:01.084Z" },
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 version = "25.4.0"
@@ -708,6 +762,8 @@ source = { editable = "packages/harness" }
 dependencies = [
     { name = "agent-client-protocol" },
     { name = "agent-sandbox" },
+    { name = "aiosqlite" },
+    { name = "alembic" },
     { name = "ddgs" },
     { name = "dotenv" },
     { name = "duckdb" },
@@ -731,14 +787,23 @@ dependencies = [
     { name = "pydantic" },
     { name = "pyyaml" },
     { name = "readabilipy" },
+    { name = "sqlalchemy", extra = ["asyncio"] },
     { name = "tavily-python" },
     { name = "tiktoken" },
 ]
 
+[package.optional-dependencies]
+postgres = [
+    { name = "asyncpg" },
+]
+
 [package.metadata]
 requires-dist = [
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     { name = "agent-sandbox", specifier = ">=0.0.19" },
+    { name = "aiosqlite", specifier = ">=0.19" },
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+    { name = "asyncpg", marker = "extra == 'postgres'", specifier = ">=0.29" },
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     { name = "dotenv", specifier = ">=0.9.9" },
     { name = "duckdb", specifier = ">=1.4.4" },
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     { name = "pyyaml", specifier = ">=6.0.3" },
     { name = "readabilipy", specifier = ">=0.3.0" },
+    { name = "sqlalchemy", extras = ["asyncio"], specifier = ">=2.0,<3.0" },
     { name = "tavily-python", specifier = ">=0.7.17" },
     { name = "tiktoken", specifier = ">=0.8.0" },
 ]
+provides-extras = ["postgres"]
 
 [[package]]
 name = "defusedxml"
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+]
+
+[package.optional-dependencies]
+asyncio = [
+    { name = "greenlet" },
+]
+
 [[package]]
 name = "sqlite-vec"
 version = "0.1.6"
diff --git a/config.example.yaml b/config.example.yaml
index b2ccfd4cc..85c625299 100644
--- a/config.example.yaml
+++ b/config.example.yaml
@@ -584,6 +584,35 @@ checkpointer:
 #   type: postgres
 #   connection_string: postgresql://user:password@localhost:5432/deerflow
 
+# ============================================================================
+# Database
+# ============================================================================
+# Unified storage backend for LangGraph checkpointer and DeerFlow
+# application data (runs, threads metadata, etc.).
+#
+# backend: memory  -- No persistence, data lost on restart (default)
+# backend: sqlite  -- Single-node deployment, files in sqlite_dir
+# backend: postgres -- Production multi-node deployment
+#
+# SQLite mode automatically uses separate .db files for checkpointer
+# and application data to avoid write-lock contention.
+#
+# Postgres mode: put your connection URL in .env as DATABASE_URL,
+# then reference it here with $DATABASE_URL.
+# Install the postgres driver: uv sync --extra postgres
+#
+# NOTE: When both `checkpointer` and `database` are configured,
+# `checkpointer` takes precedence for LangGraph state persistence.
+# If you use `database`, you can remove the `checkpointer` section.
+#
+# database:
+#   backend: sqlite
+#   sqlite_dir: ./data
+#
+# database:
+#   backend: postgres
+#   postgres_url: $DATABASE_URL
+
 # ============================================================================
 # IM Channels Configuration
 # ============================================================================