diff --git a/strix/config/loader.py b/strix/config/loader.py
index fbcde898..1b047db1 100644
--- a/strix/config/loader.py
+++ b/strix/config/loader.py
@@ -54,12 +54,19 @@ def apply_config_override(path: Path) -> None:
 
 
 def persist_current() -> None:
-    """Write currently-set env vars to the active config file (0o600)."""
+    """Write currently-set env vars to the active config file (0o600).
+
+    The existing ``"env"`` block on disk is merged in first so keys that are
+    not present in the current process environment (e.g. loaded only from the
+    file itself, or written by a newer version) are preserved. Current env
+    vars still win on conflicts. If the file is missing or contains invalid
+    JSON, behavior is unchanged: only the env-derived block is written.
+    """
     s = load_settings()
     target = _override or _DEFAULT_PATH
     target.parent.mkdir(parents=True, exist_ok=True)
 
-    env_block: dict[str, str] = {}
+    env_block: dict[str, str] = _read_existing_env_block(target)
     for sub_name in s.model_fields:
         sub_model = getattr(s, sub_name)
         if not isinstance(sub_model, BaseModel):
@@ -74,6 +81,24 @@ def persist_current() -> None:
     write_secret_text(target, json.dumps({"env": env_block}, indent=2))
 
 
+def _read_existing_env_block(path: Path) -> dict[str, str]:
+    """Return the ``"env"`` block already stored in ``path``.
+
+    Missing files, invalid JSON, and non-dict ``"env"`` values all yield an
+    empty dict so persistence degrades to the previous overwrite behavior.
+    """
+    if not path.exists():
+        return {}
+    try:
+        data = json.loads(path.read_text(encoding="utf-8"))
+    except (json.JSONDecodeError, OSError):
+        return {}
+    env_block = data.get("env", {}) if isinstance(data, dict) else {}
+    if not isinstance(env_block, dict):
+        return {}
+    return {str(k): str(v) for k, v in env_block.items()}
+
+
 def _aliases_for(finfo: FieldInfo) -> list[str]:
     """Collect every env-var name that should populate ``finfo``."""
     aliases: list[str] = []
diff --git a/tests/test_config_loader.py b/tests/test_config_loader.py
index e83ab119..023f9e78 100644
--- a/tests/test_config_loader.py
+++ b/tests/test_config_loader.py
@@ -216,3 +216,53 @@ def test_persist_current_sets_0600_mode(tmp_path: Path, monkeypatch: pytest.Monk
     loader.persist_current()
 
     assert target.stat().st_mode & 0o777 == 0o600
+
+
+def test_persist_current_preserves_file_only_keys(tmp_path: Path) -> None:
+    # Keys stored in the file but absent from the current environment (e.g.
+    # STRIX_LLM in a bare shell/cron/CI run) must survive a persist.
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps({"env": {"STRIX_LLM": "file-model", "PERPLEXITY_API_KEY": "pk"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+
+    loader.persist_current()
+
+    stored = json.loads(target.read_text(encoding="utf-8"))["env"]
+    assert stored["STRIX_LLM"] == "file-model"
+    assert stored["PERPLEXITY_API_KEY"] == "pk"
+
+
+def test_persist_current_env_var_overrides_stored_value(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.setenv("STRIX_LLM", "env-model")
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps({"env": {"STRIX_LLM": "file-model"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+
+    loader.persist_current()
+
+    stored = json.loads(target.read_text(encoding="utf-8"))["env"]
+    assert stored["STRIX_LLM"] == "env-model"
+
+
+def test_persist_current_keeps_unknown_stored_keys(tmp_path: Path) -> None:
+    # Keys outside the current schema (written by a newer version) must not
+    # be dropped by an older binary rewriting the file.
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps({"env": {"STRIX_LLM": "file-model", "FUTURE_OPTION": "on"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+
+    loader.persist_current()
+
+    stored = json.loads(target.read_text(encoding="utf-8"))["env"]
+    assert stored["FUTURE_OPTION"] == "on"