diff --git a/strix/config/loader.py b/strix/config/loader.py
index 9d9911558..5b940760f 100644
--- a/strix/config/loader.py
+++ b/strix/config/loader.py
@@ -106,6 +106,7 @@ def _read_json_overrides(path: Path) -> dict[str, dict[str, Any]]:
         return {}
 
     env_block_upper = {str(k).upper(): v for k, v in env_block.items()}
+    env_present = {k.upper() for k in os.environ}
 
     nested: dict[str, dict[str, Any]] = {}
     for sub_name, sub_finfo in Settings.model_fields.items():
@@ -114,12 +115,12 @@ def _read_json_overrides(path: Path) -> dict[str, dict[str, Any]]:
             continue
         sub_data: dict[str, Any] = {}
         for fname, finfo in sub_cls.model_fields.items():
-            for alias in _aliases_for(finfo):
-                key = alias.upper()
-                if key in os.environ:
-                    break  # env wins; skip JSON for this field
-                if key in env_block_upper:
-                    sub_data[fname] = env_block_upper[key]
+            aliases = [alias.upper() for alias in _aliases_for(finfo)]
+            if any(alias in env_present for alias in aliases):
+                continue  # env wins under some alias; skip the JSON file for this field
+            for alias in aliases:
+                if alias in env_block_upper:
+                    sub_data[fname] = env_block_upper[alias]
                     break
         if sub_data:
             nested[sub_name] = sub_data
diff --git a/tests/test_config_loader.py b/tests/test_config_loader.py
index 247c41ffe..56e644f3d 100644
--- a/tests/test_config_loader.py
+++ b/tests/test_config_loader.py
@@ -89,6 +89,36 @@ def test_read_json_overrides_skips_keys_already_in_environ(
     assert loader._read_json_overrides(path) == {}
 
 
+def test_read_json_overrides_env_wins_across_field_aliases(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    # api_key resolves from AliasChoices("LLM_API_KEY", "OPENAI_API_KEY"). The env
+    # sets one alias while the persisted file holds another. Env must still win, so
+    # the stale file value must not be surfaced as an init kwarg (which outranks env).
+    monkeypatch.setenv("OPENAI_API_KEY", "sk-env")
+    path = tmp_path / "cli-config.json"
+    path.write_text(json.dumps({"env": {"LLM_API_KEY": "sk-file"}}), encoding="utf-8")
+    assert loader._read_json_overrides(path) == {}
+
+
+def test_read_json_overrides_env_wins_case_insensitively(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    # Settings use case_sensitive=False, so a lowercase env var also counts as set.
+    monkeypatch.setenv("strix_llm", "from-env")
+    path = tmp_path / "cli-config.json"
+    path.write_text(json.dumps({"env": {"STRIX_LLM": "from-file"}}), encoding="utf-8")
+    assert loader._read_json_overrides(path) == {}
+
+
+def test_read_json_overrides_uses_json_when_no_alias_in_environ(tmp_path: Path) -> None:
+    # No alias of api_key is set in the environment -> the file value is used, even
+    # when it is stored under a non-first alias.
+    path = tmp_path / "cli-config.json"
+    path.write_text(json.dumps({"env": {"OPENAI_API_KEY": "sk-file"}}), encoding="utf-8")
+    assert loader._read_json_overrides(path) == {"llm": {"api_key": "sk-file"}}
+
+
 # --------------------------------------------------------------------------- #
 # _aliases_for
 # --------------------------------------------------------------------------- #