diff --git a/strix/config/config.py b/strix/config/config.py
index 782101dd..255df7c6 100644
--- a/strix/config/config.py
+++ b/strix/config/config.py
@@ -2,7 +2,7 @@ import contextlib
 import json
 import os
 from pathlib import Path
-from typing import Any
+from typing import Any, ClassVar
 
 
 STRIX_API_BASE = "https://models.strix.ai/api/v1"
@@ -56,6 +56,10 @@ class Config:
     # Config file override (set via --config CLI arg)
     _config_file_override: Path | None = None
 
+    # Tracks env vars set by the initial default-config load so they can be
+    # cleared when a --config override is later applied (avoids leakage).
+    _applied_from_default: ClassVar[dict[str, str]] = {}
+
     @classmethod
     def _tracked_names(cls) -> list[str]:
         return [
@@ -151,6 +155,11 @@ class Config:
                 os.environ[var_name] = var_value
                 applied[var_name] = var_value
 
+        # Record what was applied from the default config so it can be cleared
+        # if a --config override is later provided (prevents leakage).
+        if cls._config_file_override is None and not force:
+            cls._applied_from_default = applied
+
         return applied
 
     @classmethod
diff --git a/strix/interface/main.py b/strix/interface/main.py
index 7ac6f135..bc88da67 100644
--- a/strix/interface/main.py
+++ b/strix/interface/main.py
@@ -6,6 +6,7 @@ Strix Agent Interface
 import argparse
 import asyncio
 import logging
+import os
 import shutil
 import sys
 from pathlib import Path
@@ -528,6 +529,12 @@ def pull_docker_image() -> None:
 
 
 def apply_config_override(config_path: str) -> None:
+    # Clear env vars that were automatically applied from the default config file
+    # so they don't leak into the custom config context.
+    for var_name in Config._applied_from_default:
+        os.environ.pop(var_name, None)
+    Config._applied_from_default = {}
+
     Config._config_file_override = validate_config_file(config_path)
     apply_saved_config(force=True)