diff --git a/backend/app/channels/feishu.py b/backend/app/channels/feishu.py
index c2a637ff9..5a80016f0 100644
--- a/backend/app/channels/feishu.py
+++ b/backend/app/channels/feishu.py
@@ -13,6 +13,7 @@ from app.channels.base import Channel
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox_provider import get_sandbox_provider
 
 logger = logging.getLogger(__name__)
@@ -344,8 +345,9 @@ class FeishuChannel(Channel):
             return f"Failed to obtain the [{type}]"
 
         paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
-        uploads_dir = paths.sandbox_uploads_dir(thread_id).resolve()
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        uploads_dir = paths.sandbox_uploads_dir(thread_id, user_id=user_id).resolve()
 
         ext = "png" if type == "image" else "bin"
         raw_filename = getattr(response, "file_name", "") or f"feishu_{file_key[-12:]}.{ext}"
diff --git a/backend/app/channels/manager.py b/backend/app/channels/manager.py
index 2410dcb64..400d29d60 100644
--- a/backend/app/channels/manager.py
+++ b/backend/app/channels/manager.py
@@ -17,6 +17,7 @@ from langgraph_sdk.errors import ConflictError
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from app.channels.store import ChannelStore
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -341,14 +342,15 @@ def _resolve_attachments(thread_id: str, artifacts: list[str]) -> list[ResolvedA
 
     attachments: list[ResolvedAttachment] = []
     paths = get_paths()
-    outputs_dir = paths.sandbox_outputs_dir(thread_id).resolve()
+    user_id = get_effective_user_id()
+    outputs_dir = paths.sandbox_outputs_dir(thread_id, user_id=user_id).resolve()
     for virtual_path in artifacts:
         # Security: only allow files from the agent outputs directory
         if not virtual_path.startswith(_OUTPUTS_VIRTUAL_PREFIX):
             logger.warning("[Manager] rejected non-outputs artifact path: %s", virtual_path)
             continue
         try:
-            actual = paths.resolve_virtual_path(thread_id, virtual_path)
+            actual = paths.resolve_virtual_path(thread_id, virtual_path, user_id=user_id)
             # Verify the resolved path is actually under the outputs directory
             # (guards against path-traversal even after prefix check)
             try:
diff --git a/backend/app/gateway/path_utils.py b/backend/app/gateway/path_utils.py
index 4869c9404..ded348c78 100644
--- a/backend/app/gateway/path_utils.py
+++ b/backend/app/gateway/path_utils.py
@@ -5,6 +5,7 @@ from pathlib import Path
 from fastapi import HTTPException
 
 from deerflow.config.paths import get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 
 
 def resolve_thread_virtual_path(thread_id: str, virtual_path: str) -> Path:
@@ -22,7 +23,7 @@ def resolve_thread_virtual_path(thread_id: str, virtual_path: str) -> Path:
         HTTPException: If the path is invalid or outside allowed directories.
     """
     try:
-        return get_paths().resolve_virtual_path(thread_id, virtual_path)
+        return get_paths().resolve_virtual_path(thread_id, virtual_path, user_id=get_effective_user_id())
     except ValueError as e:
         status = 403 if "traversal" in str(e) else 400
         raise HTTPException(status_code=status, detail=str(e))
diff --git a/backend/app/gateway/routers/memory.py b/backend/app/gateway/routers/memory.py
index 6ee546924..ca9e5f5e5 100644
--- a/backend/app/gateway/routers/memory.py
+++ b/backend/app/gateway/routers/memory.py
@@ -13,6 +13,7 @@ from deerflow.agents.memory.updater import (
     update_memory_fact,
 )
 from deerflow.config.memory_config import get_memory_config
+from deerflow.runtime.user_context import get_effective_user_id
 
 router = APIRouter(prefix="/api", tags=["memory"])
 
@@ -147,7 +148,7 @@ async def get_memory() -> MemoryResponse:
         }
         ```
     """
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -167,7 +168,7 @@ async def reload_memory() -> MemoryResponse:
     Returns:
         The reloaded memory data.
     """
-    memory_data = reload_memory_data()
+    memory_data = reload_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -181,7 +182,7 @@ async def reload_memory() -> MemoryResponse:
 async def clear_memory() -> MemoryResponse:
     """Clear all persisted memory data."""
     try:
-        memory_data = clear_memory_data()
+        memory_data = clear_memory_data(user_id=get_effective_user_id())
     except OSError as exc:
         raise HTTPException(status_code=500, detail="Failed to clear memory data.") from exc
 
@@ -202,6 +203,7 @@ async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryRespo
             content=request.content,
             category=request.category,
             confidence=request.confidence,
+            user_id=get_effective_user_id(),
         )
     except ValueError as exc:
         raise _map_memory_fact_value_error(exc) from exc
@@ -221,7 +223,7 @@ async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryRespo
 async def delete_memory_fact_endpoint(fact_id: str) -> MemoryResponse:
     """Delete a single fact from memory by fact id."""
     try:
-        memory_data = delete_memory_fact(fact_id)
+        memory_data = delete_memory_fact(fact_id, user_id=get_effective_user_id())
     except KeyError as exc:
         raise HTTPException(status_code=404, detail=f"Memory fact '{fact_id}' not found.") from exc
     except OSError as exc:
@@ -245,6 +247,7 @@ async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -
             content=request.content,
             category=request.category,
             confidence=request.confidence,
+            user_id=get_effective_user_id(),
         )
     except ValueError as exc:
         raise _map_memory_fact_value_error(exc) from exc
@@ -265,7 +268,7 @@ async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -
 )
 async def export_memory() -> MemoryResponse:
     """Export the current memory data."""
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -279,7 +282,7 @@ async def export_memory() -> MemoryResponse:
 async def import_memory(request: MemoryResponse) -> MemoryResponse:
     """Import and persist memory data."""
     try:
-        memory_data = import_memory_data(request.model_dump())
+        memory_data = import_memory_data(request.model_dump(), user_id=get_effective_user_id())
     except OSError as exc:
         raise HTTPException(status_code=500, detail="Failed to import memory data.") from exc
 
@@ -337,7 +340,7 @@ async def get_memory_status() -> MemoryStatusResponse:
         Combined memory configuration and current data.
     """
     config = get_memory_config()
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
 
     return MemoryStatusResponse(
         config=MemoryConfigResponse(
diff --git a/backend/app/gateway/routers/threads.py b/backend/app/gateway/routers/threads.py
index 5eb4a30b5..3200f9a5a 100644
--- a/backend/app/gateway/routers/threads.py
+++ b/backend/app/gateway/routers/threads.py
@@ -26,6 +26,7 @@ from app.gateway.deps import get_checkpointer, get_current_user, get_feedback_re
 from app.gateway.utils import sanitize_log_param
 from deerflow.config.paths import Paths, get_paths
 from deerflow.runtime import serialize_channel_values
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/api/threads", tags=["threads"])
@@ -143,11 +144,11 @@ class ThreadHistoryRequest(BaseModel):
 # ---------------------------------------------------------------------------
 
 
-def _delete_thread_data(thread_id: str, paths: Paths | None = None) -> ThreadDeleteResponse:
+def _delete_thread_data(thread_id: str, paths: Paths | None = None, *, user_id: str | None = None) -> ThreadDeleteResponse:
     """Delete local persisted filesystem data for a thread."""
     path_manager = paths or get_paths()
     try:
-        path_manager.delete_thread_dir(thread_id)
+        path_manager.delete_thread_dir(thread_id, user_id=user_id)
     except ValueError as exc:
         raise HTTPException(status_code=422, detail=str(exc)) from exc
     except FileNotFoundError:
@@ -198,7 +199,7 @@ async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteRe
     from app.gateway.deps import get_thread_store
 
     # Clean local filesystem
-    response = _delete_thread_data(thread_id)
+    response = _delete_thread_data(thread_id, user_id=get_effective_user_id())
 
     # Remove checkpoints (best-effort)
     checkpointer = getattr(request.app.state, "checkpointer", None)
diff --git a/backend/app/gateway/routers/uploads.py b/backend/app/gateway/routers/uploads.py
index 3de297355..aa707e9ea 100644
--- a/backend/app/gateway/routers/uploads.py
+++ b/backend/app/gateway/routers/uploads.py
@@ -9,6 +9,7 @@ from pydantic import BaseModel
 
 from app.gateway.authz import require_permission
 from deerflow.config.paths import get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox_provider import get_sandbox_provider
 from deerflow.uploads.manager import (
     PathTraversalError,
@@ -69,7 +70,7 @@ async def upload_files(
         uploads_dir = ensure_uploads_dir(thread_id)
     except ValueError as e:
         raise HTTPException(status_code=400, detail=str(e))
-    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id)
+    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
     uploaded_files = []
 
     sandbox_provider = get_sandbox_provider()
@@ -147,7 +148,7 @@ async def list_uploaded_files(thread_id: str, request: Request) -> dict:
     enrich_file_listing(result, thread_id)
 
     # Gateway additionally includes the sandbox-relative path.
-    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id)
+    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
     for f in result["files"]:
         f["path"] = str(sandbox_uploads / f["filename"])
 
diff --git a/backend/packages/harness/deerflow/agents/lead_agent/prompt.py b/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
index 71af2e653..8e00e1ea4 100644
--- a/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
+++ b/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
@@ -519,12 +519,13 @@ def _get_memory_context(agent_name: str | None = None) -> str:
     try:
         from deerflow.agents.memory import format_memory_for_injection, get_memory_data
         from deerflow.config.memory_config import get_memory_config
+        from deerflow.runtime.user_context import get_effective_user_id
 
         config = get_memory_config()
         if not config.enabled or not config.injection_enabled:
             return ""
 
-        memory_data = get_memory_data(agent_name)
+        memory_data = get_memory_data(agent_name, user_id=get_effective_user_id())
         memory_content = format_memory_for_injection(memory_data, max_tokens=config.max_injection_tokens)
 
         if not memory_content.strip():
diff --git a/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py
index c25531e02..828a82621 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py
@@ -8,6 +8,7 @@ from langgraph.runtime import Runtime
 
 from deerflow.agents.thread_state import ThreadDataState
 from deerflow.config.paths import Paths, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -46,32 +47,34 @@ class ThreadDataMiddleware(AgentMiddleware[ThreadDataMiddlewareState]):
         self._paths = Paths(base_dir) if base_dir else get_paths()
         self._lazy_init = lazy_init
 
-    def _get_thread_paths(self, thread_id: str) -> dict[str, str]:
+    def _get_thread_paths(self, thread_id: str, user_id: str | None = None) -> dict[str, str]:
         """Get the paths for a thread's data directories.
 
         Args:
             thread_id: The thread ID.
+            user_id: Optional user ID for per-user path isolation.
 
         Returns:
             Dictionary with workspace_path, uploads_path, and outputs_path.
         """
         return {
-            "workspace_path": str(self._paths.sandbox_work_dir(thread_id)),
-            "uploads_path": str(self._paths.sandbox_uploads_dir(thread_id)),
-            "outputs_path": str(self._paths.sandbox_outputs_dir(thread_id)),
+            "workspace_path": str(self._paths.sandbox_work_dir(thread_id, user_id=user_id)),
+            "uploads_path": str(self._paths.sandbox_uploads_dir(thread_id, user_id=user_id)),
+            "outputs_path": str(self._paths.sandbox_outputs_dir(thread_id, user_id=user_id)),
         }
 
-    def _create_thread_directories(self, thread_id: str) -> dict[str, str]:
+    def _create_thread_directories(self, thread_id: str, user_id: str | None = None) -> dict[str, str]:
         """Create the thread data directories.
 
         Args:
             thread_id: The thread ID.
+            user_id: Optional user ID for per-user path isolation.
 
         Returns:
             Dictionary with the created directory paths.
         """
-        self._paths.ensure_thread_dirs(thread_id)
-        return self._get_thread_paths(thread_id)
+        self._paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        return self._get_thread_paths(thread_id, user_id=user_id)
 
     @override
     def before_agent(self, state: ThreadDataMiddlewareState, runtime: Runtime) -> dict | None:
@@ -84,12 +87,14 @@ class ThreadDataMiddleware(AgentMiddleware[ThreadDataMiddlewareState]):
         if thread_id is None:
             raise ValueError("Thread ID is required in runtime context or config.configurable")
 
+        user_id = get_effective_user_id()
+
         if self._lazy_init:
             # Lazy initialization: only compute paths, don't create directories
-            paths = self._get_thread_paths(thread_id)
+            paths = self._get_thread_paths(thread_id, user_id=user_id)
         else:
             # Eager initialization: create directories immediately
-            paths = self._create_thread_directories(thread_id)
+            paths = self._create_thread_directories(thread_id, user_id=user_id)
             logger.debug("Created thread data directories for thread %s", thread_id)
 
         return {
diff --git a/backend/packages/harness/deerflow/agents/middlewares/uploads_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/uploads_middleware.py
index 78c9a7b7b..6622fb695 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/uploads_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/uploads_middleware.py
@@ -10,6 +10,7 @@ from langchain_core.messages import HumanMessage
 from langgraph.runtime import Runtime
 
 from deerflow.config.paths import Paths, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.utils.file_conversion import extract_outline
 
 logger = logging.getLogger(__name__)
@@ -221,7 +222,7 @@ class UploadsMiddleware(AgentMiddleware[UploadsMiddlewareState]):
                 thread_id = get_config().get("configurable", {}).get("thread_id")
             except RuntimeError:
                 pass  # get_config() raises outside a runnable context (e.g. unit tests)
-        uploads_dir = self._paths.sandbox_uploads_dir(thread_id) if thread_id else None
+        uploads_dir = self._paths.sandbox_uploads_dir(thread_id, user_id=get_effective_user_id()) if thread_id else None
 
         # Get newly uploaded files from the current message's additional_kwargs.files
         new_files = self._files_from_kwargs(last_message, uploads_dir) or []
diff --git a/backend/packages/harness/deerflow/client.py b/backend/packages/harness/deerflow/client.py
index 950fdb085..7623c8f3e 100644
--- a/backend/packages/harness/deerflow/client.py
+++ b/backend/packages/harness/deerflow/client.py
@@ -40,6 +40,7 @@ from deerflow.config.app_config import get_app_config, reload_app_config
 from deerflow.config.extensions_config import ExtensionsConfig, SkillStateConfig, get_extensions_config, reload_extensions_config
 from deerflow.config.paths import get_paths
 from deerflow.models import create_chat_model
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.skills.installer import install_skill_from_archive
 from deerflow.uploads.manager import (
     claim_unique_filename,
@@ -769,19 +770,19 @@ class DeerFlowClient:
         """
         from deerflow.agents.memory.updater import get_memory_data
 
-        return get_memory_data()
+        return get_memory_data(user_id=get_effective_user_id())
 
     def export_memory(self) -> dict:
         """Export current memory data for backup or transfer."""
         from deerflow.agents.memory.updater import get_memory_data
 
-        return get_memory_data()
+        return get_memory_data(user_id=get_effective_user_id())
 
     def import_memory(self, memory_data: dict) -> dict:
         """Import and persist full memory data."""
         from deerflow.agents.memory.updater import import_memory_data
 
-        return import_memory_data(memory_data)
+        return import_memory_data(memory_data, user_id=get_effective_user_id())
 
     def get_model(self, name: str) -> dict | None:
         """Get a specific model's configuration by name.
@@ -956,13 +957,13 @@ class DeerFlowClient:
         """
         from deerflow.agents.memory.updater import reload_memory_data
 
-        return reload_memory_data()
+        return reload_memory_data(user_id=get_effective_user_id())
 
     def clear_memory(self) -> dict:
         """Clear all persisted memory data."""
         from deerflow.agents.memory.updater import clear_memory_data
 
-        return clear_memory_data()
+        return clear_memory_data(user_id=get_effective_user_id())
 
     def create_memory_fact(self, content: str, category: str = "context", confidence: float = 0.5) -> dict:
         """Create a single fact manually."""
@@ -1179,7 +1180,7 @@ class DeerFlowClient:
             ValueError: If the path is invalid.
         """
         try:
-            actual = get_paths().resolve_virtual_path(thread_id, path)
+            actual = get_paths().resolve_virtual_path(thread_id, path, user_id=get_effective_user_id())
         except ValueError as exc:
             if "traversal" in str(exc):
                 from deerflow.uploads.manager import PathTraversalError
diff --git a/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox_provider.py b/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox_provider.py
index 5bc3c3981..27a20c701 100644
--- a/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox_provider.py
+++ b/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox_provider.py
@@ -27,6 +27,7 @@ except ImportError:  # pragma: no cover - Windows fallback
 
 from deerflow.config import get_app_config
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox import Sandbox
 from deerflow.sandbox.sandbox_provider import SandboxProvider
 
@@ -260,15 +261,16 @@ class AioSandboxProvider(SandboxProvider):
         mounted Docker socket (DooD), the host Docker daemon can resolve the paths.
         """
         paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
 
         return [
-            (paths.host_sandbox_work_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/workspace", False),
-            (paths.host_sandbox_uploads_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/uploads", False),
-            (paths.host_sandbox_outputs_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/outputs", False),
+            (paths.host_sandbox_work_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/workspace", False),
+            (paths.host_sandbox_uploads_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/uploads", False),
+            (paths.host_sandbox_outputs_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/outputs", False),
             # ACP workspace: read-only inside the sandbox (lead agent reads results;
             # the ACP subprocess writes from the host side, not from within the container).
-            (paths.host_acp_workspace_dir(thread_id), "/mnt/acp-workspace", True),
+            (paths.host_acp_workspace_dir(thread_id, user_id=user_id), "/mnt/acp-workspace", True),
         ]
 
     @staticmethod
@@ -480,8 +482,9 @@ class AioSandboxProvider(SandboxProvider):
         across multiple processes, preventing container-name conflicts.
         """
         paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
-        lock_path = paths.thread_dir(thread_id) / f"{sandbox_id}.lock"
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        lock_path = paths.thread_dir(thread_id, user_id=user_id) / f"{sandbox_id}.lock"
 
         with open(lock_path, "a", encoding="utf-8") as lock_file:
             locked = False
diff --git a/backend/packages/harness/deerflow/sandbox/tools.py b/backend/packages/harness/deerflow/sandbox/tools.py
index 089fa725d..601a7efb8 100644
--- a/backend/packages/harness/deerflow/sandbox/tools.py
+++ b/backend/packages/harness/deerflow/sandbox/tools.py
@@ -200,8 +200,9 @@ def _get_acp_workspace_host_path(thread_id: str | None = None) -> str | None:
     if thread_id is not None:
         try:
             from deerflow.config.paths import get_paths
+            from deerflow.runtime.user_context import get_effective_user_id
 
-            host_path = get_paths().acp_workspace_dir(thread_id)
+            host_path = get_paths().acp_workspace_dir(thread_id, user_id=get_effective_user_id())
             if host_path.exists():
                 return str(host_path)
         except Exception:
diff --git a/backend/packages/harness/deerflow/tools/builtins/invoke_acp_agent_tool.py b/backend/packages/harness/deerflow/tools/builtins/invoke_acp_agent_tool.py
index baf7f8ff5..618649020 100644
--- a/backend/packages/harness/deerflow/tools/builtins/invoke_acp_agent_tool.py
+++ b/backend/packages/harness/deerflow/tools/builtins/invoke_acp_agent_tool.py
@@ -33,11 +33,12 @@ def _get_work_dir(thread_id: str | None) -> str:
         An absolute physical filesystem path to use as the working directory.
     """
     from deerflow.config.paths import get_paths
+    from deerflow.runtime.user_context import get_effective_user_id
 
     paths = get_paths()
     if thread_id:
         try:
-            work_dir = paths.acp_workspace_dir(thread_id)
+            work_dir = paths.acp_workspace_dir(thread_id, user_id=get_effective_user_id())
         except ValueError:
             logger.warning("Invalid thread_id %r for ACP workspace, falling back to global", thread_id)
             work_dir = paths.base_dir / "acp-workspace"
diff --git a/backend/packages/harness/deerflow/tools/builtins/present_file_tool.py b/backend/packages/harness/deerflow/tools/builtins/present_file_tool.py
index 1e0c76105..39cc61c4f 100644
--- a/backend/packages/harness/deerflow/tools/builtins/present_file_tool.py
+++ b/backend/packages/harness/deerflow/tools/builtins/present_file_tool.py
@@ -8,6 +8,7 @@ from langgraph.typing import ContextT
 
 from deerflow.agents.thread_state import ThreadState
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 
 OUTPUTS_VIRTUAL_PREFIX = f"{VIRTUAL_PATH_PREFIX}/outputs"
 
@@ -47,7 +48,7 @@ def _normalize_presented_filepath(
     virtual_prefix = VIRTUAL_PATH_PREFIX.lstrip("/")
 
     if stripped == virtual_prefix or stripped.startswith(virtual_prefix + "/"):
-        actual_path = get_paths().resolve_virtual_path(thread_id, filepath)
+        actual_path = get_paths().resolve_virtual_path(thread_id, filepath, user_id=get_effective_user_id())
     else:
         actual_path = Path(filepath).expanduser().resolve()
 
diff --git a/backend/packages/harness/deerflow/uploads/manager.py b/backend/packages/harness/deerflow/uploads/manager.py
index 8c60399e7..c36151b38 100644
--- a/backend/packages/harness/deerflow/uploads/manager.py
+++ b/backend/packages/harness/deerflow/uploads/manager.py
@@ -10,6 +10,7 @@ from pathlib import Path
 from urllib.parse import quote
 
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 
 
 class PathTraversalError(ValueError):
@@ -33,7 +34,7 @@ def validate_thread_id(thread_id: str) -> None:
 def get_uploads_dir(thread_id: str) -> Path:
     """Return the uploads directory path for a thread (no side effects)."""
     validate_thread_id(thread_id)
-    return get_paths().sandbox_uploads_dir(thread_id)
+    return get_paths().sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
 
 
 def ensure_uploads_dir(thread_id: str) -> Path:
diff --git a/backend/tests/test_aio_sandbox_provider.py b/backend/tests/test_aio_sandbox_provider.py
index e797cf7e3..c7984531f 100644
--- a/backend/tests/test_aio_sandbox_provider.py
+++ b/backend/tests/test_aio_sandbox_provider.py
@@ -57,6 +57,7 @@ def test_get_thread_mounts_includes_acp_workspace(tmp_path, monkeypatch):
     """_get_thread_mounts must include /mnt/acp-workspace (read-only) for docker sandbox."""
     aio_mod = importlib.import_module("deerflow.community.aio_sandbox.aio_sandbox_provider")
     monkeypatch.setattr(aio_mod, "get_paths", lambda: Paths(base_dir=tmp_path))
+    monkeypatch.setattr(aio_mod, "get_effective_user_id", lambda: None)
 
     mounts = aio_mod.AioSandboxProvider._get_thread_mounts("thread-3")
 
@@ -95,6 +96,7 @@ def test_get_thread_mounts_preserves_windows_host_path_style(tmp_path, monkeypat
     aio_mod = importlib.import_module("deerflow.community.aio_sandbox.aio_sandbox_provider")
     monkeypatch.setenv("DEER_FLOW_HOST_BASE_DIR", r"C:\Users\demo\deer-flow\backend\.deer-flow")
     monkeypatch.setattr(aio_mod, "get_paths", lambda: Paths(base_dir=tmp_path))
+    monkeypatch.setattr(aio_mod, "get_effective_user_id", lambda: None)
 
     mounts = aio_mod.AioSandboxProvider._get_thread_mounts("thread-10")
 
diff --git a/backend/tests/test_channel_file_attachments.py b/backend/tests/test_channel_file_attachments.py
index 2843a9cd0..7273b1c82 100644
--- a/backend/tests/test_channel_file_attachments.py
+++ b/backend/tests/test_channel_file_attachments.py
@@ -231,7 +231,7 @@ class TestResolveAttachments:
         mock_paths = MagicMock()
         mock_paths.sandbox_outputs_dir.return_value = outputs_dir
 
-        def resolve_side_effect(tid, vpath):
+        def resolve_side_effect(tid, vpath, *, user_id=None):
             if "data.csv" in vpath:
                 return good_file
             return tmp_path / "missing.txt"
diff --git a/backend/tests/test_client.py b/backend/tests/test_client.py
index a9b854e8e..d22e36d17 100644
--- a/backend/tests/test_client.py
+++ b/backend/tests/test_client.py
@@ -1241,7 +1241,10 @@ class TestMemoryManagement:
         with patch("deerflow.agents.memory.updater.import_memory_data", return_value=imported) as mock_import:
             result = client.import_memory(imported)
 
-        mock_import.assert_called_once_with(imported)
+        assert mock_import.call_count == 1
+        call_args = mock_import.call_args
+        assert call_args.args == (imported,)
+        assert "user_id" in call_args.kwargs
         assert result == imported
 
     def test_reload_memory(self, client):
@@ -1487,9 +1490,12 @@ class TestUploads:
 
 class TestArtifacts:
     def test_get_artifact(self, client):
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             paths = Paths(base_dir=tmp)
-            outputs = paths.sandbox_outputs_dir("t1")
+            user_id = get_effective_user_id()
+            outputs = paths.sandbox_outputs_dir("t1", user_id=user_id)
             outputs.mkdir(parents=True)
             (outputs / "result.txt").write_text("artifact content")
 
@@ -1500,9 +1506,12 @@ class TestArtifacts:
             assert "text" in mime
 
     def test_get_artifact_not_found(self, client):
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             paths = Paths(base_dir=tmp)
-            paths.sandbox_user_data_dir("t1").mkdir(parents=True)
+            user_id = get_effective_user_id()
+            paths.sandbox_outputs_dir("t1", user_id=user_id).mkdir(parents=True)
 
             with patch("deerflow.client.get_paths", return_value=paths):
                 with pytest.raises(FileNotFoundError):
@@ -1513,9 +1522,12 @@ class TestArtifacts:
             client.get_artifact("t1", "bad/path/file.txt")
 
     def test_get_artifact_path_traversal(self, client):
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             paths = Paths(base_dir=tmp)
-            paths.sandbox_user_data_dir("t1").mkdir(parents=True)
+            user_id = get_effective_user_id()
+            paths.sandbox_outputs_dir("t1", user_id=user_id).mkdir(parents=True)
 
             with patch("deerflow.client.get_paths", return_value=paths):
                 with pytest.raises(PathTraversalError):
@@ -1699,13 +1711,16 @@ class TestScenarioFileLifecycle:
 
     def test_upload_then_read_artifact(self, client):
         """Upload a file, simulate agent producing artifact, read it back."""
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             tmp_path = Path(tmp)
             uploads_dir = tmp_path / "uploads"
             uploads_dir.mkdir()
 
             paths = Paths(base_dir=tmp_path)
-            outputs_dir = paths.sandbox_outputs_dir("t-artifact")
+            user_id = get_effective_user_id()
+            outputs_dir = paths.sandbox_outputs_dir("t-artifact", user_id=user_id)
             outputs_dir.mkdir(parents=True)
 
             # Upload phase
@@ -1955,11 +1970,14 @@ class TestScenarioThreadIsolation:
 
     def test_artifacts_isolated_per_thread(self, client):
         """Artifacts in thread-A are not accessible from thread-B."""
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             paths = Paths(base_dir=tmp)
-            outputs_a = paths.sandbox_outputs_dir("thread-a")
+            user_id = get_effective_user_id()
+            outputs_a = paths.sandbox_outputs_dir("thread-a", user_id=user_id)
             outputs_a.mkdir(parents=True)
-            paths.sandbox_user_data_dir("thread-b").mkdir(parents=True)
+            paths.sandbox_outputs_dir("thread-b", user_id=user_id).mkdir(parents=True)
             (outputs_a / "result.txt").write_text("thread-a artifact")
 
             with patch("deerflow.client.get_paths", return_value=paths):
@@ -2864,9 +2882,12 @@ class TestUploadDeleteSymlink:
 class TestArtifactHardening:
     def test_artifact_directory_rejected(self, client):
         """get_artifact rejects paths that resolve to a directory."""
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             paths = Paths(base_dir=tmp)
-            subdir = paths.sandbox_outputs_dir("t1") / "subdir"
+            user_id = get_effective_user_id()
+            subdir = paths.sandbox_outputs_dir("t1", user_id=user_id) / "subdir"
             subdir.mkdir(parents=True)
 
             with patch("deerflow.client.get_paths", return_value=paths):
@@ -2875,9 +2896,12 @@ class TestArtifactHardening:
 
     def test_artifact_leading_slash_stripped(self, client):
         """Paths with leading slash are handled correctly."""
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             paths = Paths(base_dir=tmp)
-            outputs = paths.sandbox_outputs_dir("t1")
+            user_id = get_effective_user_id()
+            outputs = paths.sandbox_outputs_dir("t1", user_id=user_id)
             outputs.mkdir(parents=True)
             (outputs / "file.txt").write_text("content")
 
@@ -2991,9 +3015,12 @@ class TestBugArtifactPrefixMatchTooLoose:
 
     def test_exact_prefix_without_subpath_accepted(self, client):
         """Bare 'mnt/user-data' is accepted (will later fail as directory, not at prefix)."""
+        from deerflow.runtime.user_context import get_effective_user_id
+
         with tempfile.TemporaryDirectory() as tmp:
             paths = Paths(base_dir=tmp)
-            paths.sandbox_user_data_dir("t1").mkdir(parents=True)
+            user_id = get_effective_user_id()
+            paths.sandbox_outputs_dir("t1", user_id=user_id).mkdir(parents=True)
 
             with patch("deerflow.client.get_paths", return_value=paths):
                 # Accepted at prefix check, but fails because it's a directory.
diff --git a/backend/tests/test_client_e2e.py b/backend/tests/test_client_e2e.py
index b26e5bff1..6c688933a 100644
--- a/backend/tests/test_client_e2e.py
+++ b/backend/tests/test_client_e2e.py
@@ -262,8 +262,9 @@ class TestFileUploadIntegration:
 
         # Physically exists
         from deerflow.config.paths import get_paths
+        from deerflow.runtime.user_context import get_effective_user_id
 
-        assert (get_paths().sandbox_uploads_dir(tid) / "readme.txt").exists()
+        assert (get_paths().sandbox_uploads_dir(tid, user_id=get_effective_user_id()) / "readme.txt").exists()
 
     def test_upload_duplicate_rename(self, e2e_env, tmp_path):
         """Uploading two files with the same name auto-renames the second."""
@@ -472,12 +473,13 @@ class TestArtifactAccess:
     def test_get_artifact_happy_path(self, e2e_env):
         """Write a file to outputs, then read it back via get_artifact()."""
         from deerflow.config.paths import get_paths
+        from deerflow.runtime.user_context import get_effective_user_id
 
         c = DeerFlowClient(checkpointer=None, thinking_enabled=False)
         tid = str(uuid.uuid4())
 
         # Create an output file in the thread's outputs directory
-        outputs_dir = get_paths().sandbox_outputs_dir(tid)
+        outputs_dir = get_paths().sandbox_outputs_dir(tid, user_id=get_effective_user_id())
         outputs_dir.mkdir(parents=True, exist_ok=True)
         (outputs_dir / "result.txt").write_text("hello artifact")
 
@@ -488,11 +490,12 @@ class TestArtifactAccess:
     def test_get_artifact_nested_path(self, e2e_env):
         """Artifacts in subdirectories are accessible."""
         from deerflow.config.paths import get_paths
+        from deerflow.runtime.user_context import get_effective_user_id
 
         c = DeerFlowClient(checkpointer=None, thinking_enabled=False)
         tid = str(uuid.uuid4())
 
-        outputs_dir = get_paths().sandbox_outputs_dir(tid)
+        outputs_dir = get_paths().sandbox_outputs_dir(tid, user_id=get_effective_user_id())
         sub = outputs_dir / "charts"
         sub.mkdir(parents=True, exist_ok=True)
         (sub / "data.json").write_text('{"x": 1}')
diff --git a/backend/tests/test_invoke_acp_agent_tool.py b/backend/tests/test_invoke_acp_agent_tool.py
index 8063875cf..3c5f6f0ff 100644
--- a/backend/tests/test_invoke_acp_agent_tool.py
+++ b/backend/tests/test_invoke_acp_agent_tool.py
@@ -152,8 +152,10 @@ def test_get_work_dir_uses_base_dir_when_no_thread_id(monkeypatch, tmp_path):
 def test_get_work_dir_uses_per_thread_path_when_thread_id_given(monkeypatch, tmp_path):
     """P1.1: _get_work_dir(thread_id) uses {base_dir}/threads/{thread_id}/acp-workspace/."""
     from deerflow.config import paths as paths_module
+    from deerflow.runtime import user_context as uc_module
 
     monkeypatch.setattr(paths_module, "get_paths", lambda: paths_module.Paths(base_dir=tmp_path))
+    monkeypatch.setattr(uc_module, "get_effective_user_id", lambda: None)
     result = _get_work_dir("thread-abc-123")
     expected = tmp_path / "threads" / "thread-abc-123" / "acp-workspace"
     assert result == str(expected)
@@ -310,8 +312,10 @@ async def test_invoke_acp_agent_uses_fixed_acp_workspace(monkeypatch, tmp_path):
 async def test_invoke_acp_agent_uses_per_thread_workspace_when_thread_id_in_config(monkeypatch, tmp_path):
     """P1.1: When thread_id is in the RunnableConfig, ACP agent uses per-thread workspace."""
     from deerflow.config import paths as paths_module
+    from deerflow.runtime import user_context as uc_module
 
     monkeypatch.setattr(paths_module, "get_paths", lambda: paths_module.Paths(base_dir=tmp_path))
+    monkeypatch.setattr(uc_module, "get_effective_user_id", lambda: None)
 
     monkeypatch.setattr(
         "deerflow.config.extensions_config.ExtensionsConfig.from_file",
diff --git a/backend/tests/test_memory_router.py b/backend/tests/test_memory_router.py
index 23a4f30fe..91fd1d662 100644
--- a/backend/tests/test_memory_router.py
+++ b/backend/tests/test_memory_router.py
@@ -258,12 +258,13 @@ def test_update_memory_fact_route_preserves_omitted_fields() -> None:
             )
 
     assert response.status_code == 200
-    update_fact.assert_called_once_with(
-        fact_id="fact_edit",
-        content="User prefers spaces",
-        category=None,
-        confidence=None,
-    )
+    assert update_fact.call_count == 1
+    call_kwargs = update_fact.call_args.kwargs
+    assert call_kwargs.get("fact_id") == "fact_edit"
+    assert call_kwargs.get("content") == "User prefers spaces"
+    assert call_kwargs.get("category") is None
+    assert call_kwargs.get("confidence") is None
+    assert "user_id" in call_kwargs
     assert response.json()["facts"] == updated_memory["facts"]
 
 
diff --git a/backend/tests/test_present_file_tool_core_logic.py b/backend/tests/test_present_file_tool_core_logic.py
index 3068ca507..de1a90e52 100644
--- a/backend/tests/test_present_file_tool_core_logic.py
+++ b/backend/tests/test_present_file_tool_core_logic.py
@@ -38,7 +38,7 @@ def test_present_files_keeps_virtual_outputs_path(tmp_path, monkeypatch):
     monkeypatch.setattr(
         present_file_tool_module,
         "get_paths",
-        lambda: SimpleNamespace(resolve_virtual_path=lambda thread_id, path: artifact_path),
+        lambda: SimpleNamespace(resolve_virtual_path=lambda thread_id, path, *, user_id=None: artifact_path),
     )
 
     result = present_file_tool_module.present_file_tool.func(
diff --git a/backend/tests/test_threads_router.py b/backend/tests/test_threads_router.py
index c6f063e32..4ffa28a8c 100644
--- a/backend/tests/test_threads_router.py
+++ b/backend/tests/test_threads_router.py
@@ -50,10 +50,13 @@ def test_delete_thread_data_rejects_invalid_thread_id(tmp_path):
 
 
 def test_delete_thread_route_cleans_thread_directory(tmp_path):
+    from deerflow.runtime.user_context import get_effective_user_id
+
     paths = Paths(tmp_path)
-    thread_dir = paths.thread_dir("thread-route")
-    paths.sandbox_work_dir("thread-route").mkdir(parents=True, exist_ok=True)
-    (paths.sandbox_work_dir("thread-route") / "notes.txt").write_text("hello", encoding="utf-8")
+    user_id = get_effective_user_id()
+    thread_dir = paths.thread_dir("thread-route", user_id=user_id)
+    paths.sandbox_work_dir("thread-route", user_id=user_id).mkdir(parents=True, exist_ok=True)
+    (paths.sandbox_work_dir("thread-route", user_id=user_id) / "notes.txt").write_text("hello", encoding="utf-8")
 
     app = make_authed_test_app()
     app.include_router(threads.router)
diff --git a/backend/tests/test_uploads_middleware_core_logic.py b/backend/tests/test_uploads_middleware_core_logic.py
index 72639fb09..2c562b179 100644
--- a/backend/tests/test_uploads_middleware_core_logic.py
+++ b/backend/tests/test_uploads_middleware_core_logic.py
@@ -34,7 +34,9 @@ def _runtime(thread_id: str | None = THREAD_ID) -> MagicMock:
 
 
 def _uploads_dir(tmp_path: Path, thread_id: str = THREAD_ID) -> Path:
-    d = Paths(str(tmp_path)).sandbox_uploads_dir(thread_id)
+    from deerflow.runtime.user_context import get_effective_user_id
+
+    d = Paths(str(tmp_path)).sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
     d.mkdir(parents=True, exist_ok=True)
     return d