diff --git a/strix/config/loader.py b/strix/config/loader.py
index 5c8f9670..03c59ea0 100644
--- a/strix/config/loader.py
+++ b/strix/config/loader.py
@@ -63,7 +63,7 @@ def persist_current() -> None:
     target = _override or _DEFAULT_PATH
     target.parent.mkdir(parents=True, exist_ok=True)
 
-    env_block: dict[str, str] = _read_persisted_env(target)
+    env_block: dict[str, Any] = _read_persisted_env(target)
     for sub_name in s.model_fields:
         sub_model = getattr(s, sub_name)
         if not isinstance(sub_model, BaseModel):
@@ -78,7 +78,7 @@ def persist_current() -> None:
     write_secret_text(target, json.dumps({"env": env_block}, indent=2))
 
 
-def _read_persisted_env(path: Path) -> dict[str, str]:
+def _read_persisted_env(path: Path) -> dict[str, Any]:
     """Read the ``{"env": {...}}`` block already stored at ``path``."""
     if not path.exists():
         return {}
@@ -90,9 +90,9 @@ def _read_persisted_env(path: Path) -> dict[str, str]:
     if not isinstance(env_block, dict):
         return {}
     return {
-        str(key).upper(): str(value)
+        str(key).upper(): value
         for key, value in env_block.items()
-        if isinstance(value, str | int | float) and str(value)
+        if value is not None and value != ""
     }
 
 
diff --git a/tests/test_config_loader.py b/tests/test_config_loader.py
index 38a65040..5b70fc5d 100644
--- a/tests/test_config_loader.py
+++ b/tests/test_config_loader.py
@@ -245,6 +245,32 @@ def test_persist_current_env_wins_over_persisted_value(
     assert json.loads(target.read_text(encoding="utf-8"))["env"]["STRIX_LLM"] == "env-model"
 
 
+def test_persist_current_preserves_dict_valued_key(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.delenv("STRIX_LLM", raising=False)
+    monkeypatch.delenv("LLM_EXTRA_HEADERS", raising=False)
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps(
+            {
+                "env": {
+                    "STRIX_LLM": "file-model",
+                    "LLM_EXTRA_HEADERS": {"X-Foo": "bar"},
+                }
+            }
+        ),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+
+    loader.persist_current()
+
+    persisted_env = json.loads(target.read_text(encoding="utf-8"))["env"]
+    assert persisted_env["STRIX_LLM"] == "file-model"
+    assert persisted_env["LLM_EXTRA_HEADERS"] == {"X-Foo": "bar"}
+
+
 def test_persist_current_sets_0600_mode(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
     monkeypatch.setenv("STRIX_LLM", "persisted-model")
     target = tmp_path / "cli-config.json"