diff --git a/src/haiku/rag/config/__init__.py b/src/haiku/rag/config/__init__.py
index e0299a6f..d8d672d2 100644
--- a/src/haiku/rag/config/__init__.py
+++ b/src/haiku/rag/config/__init__.py
@@ -1,7 +1,6 @@
 import os
 
 from haiku.rag.config.loader import (
-    check_for_deprecated_env,
     find_config_file,
     generate_default_config,
     load_config_from_env,
@@ -49,6 +48,3 @@ if config_path:
     Config = AppConfig.model_validate(yaml_data)
 else:
     Config = AppConfig()
-
-# Check for deprecated .env file
-check_for_deprecated_env()
diff --git a/src/haiku/rag/config/loader.py b/src/haiku/rag/config/loader.py
index 33d3dcd4..70e91b32 100644
--- a/src/haiku/rag/config/loader.py
+++ b/src/haiku/rag/config/loader.py
@@ -1,5 +1,4 @@
 import os
-import warnings
 from pathlib import Path
 
 import yaml
@@ -45,19 +44,6 @@ def load_yaml_config(path: Path) -> dict:
     return data or {}
 
 
-def check_for_deprecated_env() -> None:
-    """Check for .env file and warn if found."""
-    env_file = Path.cwd() / ".env"
-    if env_file.exists():
-        warnings.warn(
-            ".env file detected but YAML configuration is now preferred. "
-            "Environment variable configuration is deprecated and will be removed in future versions."
-            "Run 'haiku-rag init-config' to generate a YAML config file.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
-
 def generate_default_config() -> dict:
     """Generate a default YAML config structure with documentation."""
     return {