diff --git a/backend/packages/harness/deerflow/config/app_config.py b/backend/packages/harness/deerflow/config/app_config.py
index c190d419c..5e31c3e37 100644
--- a/backend/packages/harness/deerflow/config/app_config.py
+++ b/backend/packages/harness/deerflow/config/app_config.py
@@ -33,6 +33,12 @@ load_dotenv()
 logger = logging.getLogger(__name__)
 
 
+CONFIG_FILE_DATABASE_DEFAULTS = {
+    "backend": "sqlite",
+    "sqlite_dir": ".deer-flow/data",
+}
+
+
 class CircuitBreakerConfig(BaseModel):
     """Configuration for the LLM Circuit Breaker."""
 
@@ -118,6 +124,7 @@ class AppConfig(BaseModel):
         cls._check_config_version(config_data, resolved_path)
 
         config_data = cls.resolve_env_variables(config_data)
+        cls._apply_database_defaults(config_data)
 
         # Load title config if present
         if "title" in config_data:
@@ -169,6 +176,18 @@ class AppConfig(BaseModel):
         result = cls.model_validate(config_data)
         return result
 
+    @classmethod
+    def _apply_database_defaults(cls, config_data: dict[str, Any]) -> None:
+        """Apply config.yaml defaults for persistence when the section is absent."""
+        database_config = config_data.get("database")
+        if database_config is None:
+            database_config = {}
+            config_data["database"] = database_config
+        if not isinstance(database_config, dict):
+            return
+        for key, value in CONFIG_FILE_DATABASE_DEFAULTS.items():
+            database_config.setdefault(key, value)
+
     @classmethod
     def _check_config_version(cls, config_data: dict, config_path: Path) -> None:
         """Check if the user's config.yaml is outdated compared to config.example.yaml.
diff --git a/backend/tests/test_app_config_reload.py b/backend/tests/test_app_config_reload.py
index 9e865f142..31e571afe 100644
--- a/backend/tests/test_app_config_reload.py
+++ b/backend/tests/test_app_config_reload.py
@@ -7,7 +7,7 @@ from pathlib import Path
 import yaml
 
 from deerflow.config.agents_api_config import get_agents_api_config
-from deerflow.config.app_config import get_app_config, reset_app_config
+from deerflow.config.app_config import AppConfig, get_app_config, reset_app_config
 
 
 def _write_config(path: Path, *, model_name: str, supports_thinking: bool) -> None:
@@ -57,6 +57,42 @@ def _write_extensions_config(path: Path) -> None:
     path.write_text(json.dumps({"mcpServers": {}, "skills": {}}), encoding="utf-8")
 
 
+def test_app_config_defaults_missing_database_to_sqlite(tmp_path, monkeypatch):
+    config_path = tmp_path / "config.yaml"
+    extensions_path = tmp_path / "extensions_config.json"
+    _write_extensions_config(extensions_path)
+    _write_config(config_path, model_name="first-model", supports_thinking=False)
+
+    monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(extensions_path))
+
+    config = AppConfig.from_file(str(config_path))
+
+    assert config.database.backend == "sqlite"
+    assert config.database.sqlite_dir == ".deer-flow/data"
+
+
+def test_app_config_defaults_empty_database_to_sqlite(tmp_path, monkeypatch):
+    config_path = tmp_path / "config.yaml"
+    extensions_path = tmp_path / "extensions_config.json"
+    _write_extensions_config(extensions_path)
+    config_path.write_text(
+        yaml.safe_dump(
+            {
+                "database": {},
+                "sandbox": {"use": "deerflow.sandbox.local:LocalSandboxProvider"},
+            }
+        ),
+        encoding="utf-8",
+    )
+
+    monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(extensions_path))
+
+    config = AppConfig.from_file(str(config_path))
+
+    assert config.database.backend == "sqlite"
+    assert config.database.sqlite_dir == ".deer-flow/data"
+
+
 def test_get_app_config_reloads_when_file_changes(tmp_path, monkeypatch):
     config_path = tmp_path / "config.yaml"
     extensions_path = tmp_path / "extensions_config.json"
diff --git a/config.example.yaml b/config.example.yaml
index 366e755ed..0b72ab80f 100644
--- a/config.example.yaml
+++ b/config.example.yaml
@@ -816,10 +816,14 @@ skill_evolution:
 # Unified storage backend for LangGraph checkpointer and DeerFlow
 # application data (runs, threads metadata, feedback, etc.).
 #
-# backend: memory  -- No persistence, data lost on restart (default)
+# backend: memory  -- No persistence, data lost on restart
 # backend: sqlite  -- Single-node deployment, files in sqlite_dir
 # backend: postgres -- Production multi-node deployment
 #
+# If this section is omitted or empty in config.yaml, DeerFlow uses:
+#   backend: sqlite
+#   sqlite_dir: .deer-flow/data
+#
 # SQLite mode uses a single deerflow.db file with WAL journal mode
 # for both checkpointer and application data.
 #