diff --git a/cognee-mcp/entrypoint.sh b/cognee-mcp/entrypoint.sh
index 53da83c11..e3ff849e0 100644
--- a/cognee-mcp/entrypoint.sh
+++ b/cognee-mcp/entrypoint.sh
@@ -48,27 +48,27 @@ if [ "$ENVIRONMENT" = "dev" ] || [ "$ENVIRONMENT" = "local" ]; then
     if [ "$DEBUG" = "true" ]; then
         echo "Waiting for the debugger to attach..."
         if [ "$TRANSPORT_MODE" = "sse" ]; then
-            exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport sse --host 0.0.0.0 --port $HTTP_PORT --no-migration
+            exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee-mcp --transport sse --host 0.0.0.0 --port $HTTP_PORT --no-migration
         elif [ "$TRANSPORT_MODE" = "http" ]; then
-            exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
+            exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee-mcp --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
         else
-            exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport stdio --no-migration
+            exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee-mcp --transport stdio --no-migration
         fi
     else
         if [ "$TRANSPORT_MODE" = "sse" ]; then
-            exec cognee --transport sse --host 0.0.0.0 --port $HTTP_PORT --no-migration
+            exec cognee-mcp --transport sse --host 0.0.0.0 --port $HTTP_PORT --no-migration
         elif [ "$TRANSPORT_MODE" = "http" ]; then
-            exec cognee --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
+            exec cognee-mcp --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
         else
-            exec cognee --transport stdio --no-migration
+            exec cognee-mcp --transport stdio --no-migration
         fi
     fi
 else
     if [ "$TRANSPORT_MODE" = "sse" ]; then
-        exec cognee --transport sse --host 0.0.0.0 --port $HTTP_PORT --no-migration
+        exec cognee-mcp --transport sse --host 0.0.0.0 --port $HTTP_PORT --no-migration
     elif [ "$TRANSPORT_MODE" = "http" ]; then
-        exec cognee --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
+        exec cognee-mcp --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
     else
-        exec cognee --transport stdio --no-migration
+        exec cognee-mcp --transport stdio --no-migration
     fi
 fi
diff --git a/cognee-mcp/pyproject.toml b/cognee-mcp/pyproject.toml
index 8d9373bc9..5c92deac8 100644
--- a/cognee-mcp/pyproject.toml
+++ b/cognee-mcp/pyproject.toml
@@ -37,3 +37,4 @@ allow-direct-references = true
 
 [project.scripts]
 cognee = "src:main"
+cognee-mcp = "src:main_mcp"
diff --git a/cognee-mcp/src/__init__.py b/cognee-mcp/src/__init__.py
index 1939efe9f..c71afdd1b 100644
--- a/cognee-mcp/src/__init__.py
+++ b/cognee-mcp/src/__init__.py
@@ -1,8 +1,28 @@
 from .server import main as server_main
+import warnings
 
 
 def main():
-    """Main entry point for the package."""
+    """Deprecated main entry point for the package."""
+    import asyncio
+
+    # Show deprecation warning
+    warnings.warn(
+        "The 'cognee' command for cognee-mcp is deprecated and will be removed in a future version. "
+        "Please use 'cognee-mcp' instead to avoid conflicts with the main cognee library.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+
+    print("⚠️  DEPRECATION WARNING: Use 'cognee-mcp' command instead of 'cognee'")
+    print("   This avoids conflicts with the main cognee library.")
+    print()
+
+    asyncio.run(server_main())
+
+
+def main_mcp():
+    """Clean main entry point for cognee-mcp command."""
     import asyncio
 
     asyncio.run(server_main())