diff --git a/src/basic_memory/api/app.py b/src/basic_memory/api/app.py
index 597f646bc..626a91a18 100644
--- a/src/basic_memory/api/app.py
+++ b/src/basic_memory/api/app.py
@@ -22,18 +22,19 @@
     webdav,
 )
 from basic_memory.config import ConfigManager
-from basic_memory.services.initialization import initialize_file_sync
+from basic_memory.services.initialization import initialize_file_sync, initialize_app
 
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):  # pragma: no cover
-    """Lifecycle manager for the FastAPI app."""
+    """Lifecycle manager for the FastAPI app. Not called in stdio mcp mode"""
 
     app_config = ConfigManager().config
     logger.info("Starting Basic Memory API")
-    print(f"fastapi {app_config.projects}")
 
-    # Cache database connections in app state for performance (no project reconciliation)
+    await initialize_app(app_config)
+
+    # Cache database connections in app state for performance
     logger.info("Initializing database and caching connections...")
     engine, session_maker = await db.get_or_create_db(app_config.database_path)
     app.state.engine = engine
diff --git a/src/basic_memory/cli/commands/mcp.py b/src/basic_memory/cli/commands/mcp.py
index 44561a331..3b3ea32c0 100644
--- a/src/basic_memory/cli/commands/mcp.py
+++ b/src/basic_memory/cli/commands/mcp.py
@@ -17,6 +17,8 @@
 # Import prompts to register them
 import basic_memory.mcp.prompts  # noqa: F401  # pragma: no cover
 from loguru import logger
+import threading
+from basic_memory.services.initialization import initialize_file_sync
 
 
 @app.command()
@@ -50,10 +52,6 @@ def mcp(
         os.environ["BASIC_MEMORY_MCP_PROJECT"] = project_name
         logger.info(f"MCP server constrained to project: {project_name}")
 
-    # Use unified thread-based sync approach for both transports
-    import threading
-    from basic_memory.services.initialization import initialize_file_sync
-
     app_config = ConfigManager().config
 
     def run_file_sync():
diff --git a/src/basic_memory/mcp/server.py b/src/basic_memory/mcp/server.py
index 1125ab0ec..e1dfaebb9 100644
--- a/src/basic_memory/mcp/server.py
+++ b/src/basic_memory/mcp/server.py
@@ -2,39 +2,8 @@
 Basic Memory FastMCP server.
 """
 
-import asyncio
-from contextlib import asynccontextmanager
-from dataclasses import dataclass
-from typing import AsyncIterator, Optional, Any
-
 from fastmcp import FastMCP
 
-from basic_memory.config import ConfigManager
-from basic_memory.services.initialization import initialize_app
-
-
-@dataclass
-class AppContext:
-    watch_task: Optional[asyncio.Task]
-    migration_manager: Optional[Any] = None
-
-
-@asynccontextmanager
-async def app_lifespan(server: FastMCP) -> AsyncIterator[AppContext]:  # pragma: no cover
-    """ """
-    app_config = ConfigManager().config
-    # Initialize on startup (now returns migration_manager)
-    migration_manager = await initialize_app(app_config)
-
-    try:
-        yield AppContext(watch_task=None, migration_manager=migration_manager)
-    finally:
-        # Cleanup on shutdown - migration tasks will be cancelled automatically
-        pass
-
-
-# Create the shared server instance with custom Stytch auth
 mcp = FastMCP(
     name="Basic Memory",
-    lifespan=app_lifespan,
 )