diff --git a/tests/config/test_config_override.py b/tests/config/test_config_override.py
new file mode 100644
index 00000000..ca16e7e4
--- /dev/null
+++ b/tests/config/test_config_override.py
@@ -0,0 +1,31 @@
+import json
+import os
+import sys
+
+from strix.config.config import Config
+
+
+def test_apply_config_override_clears_default_only_vars(monkeypatch, tmp_path) -> None:
+    default_cfg = tmp_path / "cli-config.json"
+    default_cfg.write_text(
+        json.dumps({"env": {"LLM_API_BASE": "https://default.api", "STRIX_LLM": "default-model"}}),
+        encoding="utf-8",
+    )
+    custom_cfg = tmp_path / "custom.json"
+    custom_cfg.write_text(json.dumps({"env": {"STRIX_LLM": "custom-model"}}), encoding="utf-8")
+
+    monkeypatch.setattr(Config, "_config_file_override", None)
+    monkeypatch.setattr(Config, "_applied_from_default", {})
+    monkeypatch.setattr(Config, "config_dir", classmethod(lambda cls: tmp_path))
+    for var_name in Config._llm_env_vars():
+        monkeypatch.delenv(var_name, raising=False)
+    sys.modules.pop("strix.interface.main", None)
+
+    from strix.interface.main import apply_config_override
+
+    assert os.environ.get("LLM_API_BASE") == "https://default.api"
+
+    apply_config_override(str(custom_cfg))
+
+    assert os.environ.get("STRIX_LLM") == "custom-model"
+    assert "LLM_API_BASE" not in os.environ