diff --git a/cognee-mcp/entrypoint.sh b/cognee-mcp/entrypoint.sh
index 1d762242b..60b6ad459 100644
--- a/cognee-mcp/entrypoint.sh
+++ b/cognee-mcp/entrypoint.sh
@@ -58,14 +58,20 @@ else
     echo "Direct mode: Using local cognee instance"
     echo "Running database migrations..."
 
+    set +e # Disable exit on error to handle specific migration errors
     MIGRATION_OUTPUT=$(cd cognee && alembic upgrade head)
     MIGRATION_EXIT_CODE=$?
+    set -e
 
     if [[ $MIGRATION_EXIT_CODE -ne 0 ]]; then
-        if [[ "$MIGRATION_OUTPUT" == *"UserAlreadyExists"* ]] || [[ "$MIGRATION_OUTPUT" == *"User default_user@example.com already exists"* ]]; then
-            echo "Warning: Default user already exists, continuing startup..."
-        else
-            echo "Migration failed with unexpected error."
+
+        echo "Migration failed with unexpected error. Trying to run Cognee without migrations."
+        echo "Initializing database tables..."
+        python /app/src/run_cognee_database_setup.py
+        INIT_EXIT_CODE=$?
+
+        if [[ $INIT_EXIT_CODE -ne 0 ]]; then
+            echo "Database initialization failed!"
             exit 1
         fi
     fi
diff --git a/cognee-mcp/src/run_cognee_database_setup.py b/cognee-mcp/src/run_cognee_database_setup.py
new file mode 100644
index 000000000..e0ac91ec4
--- /dev/null
+++ b/cognee-mcp/src/run_cognee_database_setup.py
@@ -0,0 +1,5 @@
+from cognee.modules.engine.operations.setup import setup
+import asyncio
+
+if __name__ == "__main__":
+    asyncio.run(setup())
diff --git a/entrypoint.sh b/entrypoint.sh
index 0a6d1cb25..ed7e6b15d 100755
--- a/entrypoint.sh
+++ b/entrypoint.sh
@@ -20,19 +20,15 @@ MIGRATION_EXIT_CODE=$?
 set -e
 
 if [[ $MIGRATION_EXIT_CODE -ne 0 ]]; then
-    if [[ "$MIGRATION_OUTPUT" == *"UserAlreadyExists"* ]] || [[ "$MIGRATION_OUTPUT" == *"User default_user@example.com already exists"* ]]; then
-        echo "Warning: Default user already exists, continuing startup..."
-    else
-        echo "Migration failed with unexpected error. Trying to run Cognee without migrations."
+    echo "Migration failed with unexpected error. Trying to run Cognee without migrations."
 
-        echo "Initializing database tables..."
-        python /app/cognee/modules/engine/operations/setup.py
-        INIT_EXIT_CODE=$?
+    echo "Initializing database tables..."
+    python /app/cognee/modules/engine/operations/setup.py
+    INIT_EXIT_CODE=$?
 
-        if [[ $INIT_EXIT_CODE -ne 0 ]]; then
-            echo "Database initialization failed!"
-            exit 1
-        fi
+    if [[ $INIT_EXIT_CODE -ne 0 ]]; then
+        echo "Database initialization failed!"
+        exit 1
     fi
 else
     echo "Database migrations done."