diff --git a/cognee-mcp/pyproject.toml b/cognee-mcp/pyproject.toml
index e1a3a092c..5c92deac8 100644
--- a/cognee-mcp/pyproject.toml
+++ b/cognee-mcp/pyproject.toml
@@ -36,4 +36,5 @@ dev = [
 allow-direct-references = true
 
 [project.scripts]
-cognee-mcp = "src:main"
+cognee = "src:main"
+cognee-mcp = "src:main_mcp"
diff --git a/cognee-mcp/src/__init__.py b/cognee-mcp/src/__init__.py
index 1939efe9f..32a291cfb 100644
--- a/cognee-mcp/src/__init__.py
+++ b/cognee-mcp/src/__init__.py
@@ -1,8 +1,27 @@
 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())