diff --git a/apps/server/src/config.ts b/apps/server/src/config.ts
index 0b25b3ccc..34f19fabd 100644
--- a/apps/server/src/config.ts
+++ b/apps/server/src/config.ts
@@ -1,7 +1,28 @@
-import { existsSync } from "node:fs";
+import { existsSync, readFileSync } from "node:fs";
 import { resolve } from "node:path";
+import { parseEnv } from "node:util";
 
-if (existsSync(".env")) process.loadEnvFile(".env");
+/** .env keys whose file value loses to a different value already set in the environment. */
+export function shadowedEnvKeys(
+  file: Record<string, string | undefined>,
+  env: Record<string, string | undefined> = process.env,
+): string[] {
+  return Object.keys(file).filter((key) => env[key] !== undefined && env[key] !== file[key]);
+}
+
+if (existsSync(".env")) {
+  // loadEnvFile never overrides existing variables. A stale shell or system-wide value
+  // (for example OPENAI_API_KEY) would otherwise silently replace the .env setting.
+  const shadowed = shadowedEnvKeys(parseEnv(readFileSync(".env", "utf8")));
+  process.loadEnvFile(".env");
+  if (shadowed.length)
+    console.warn(
+      `[OpenMuse] Using ${shadowed.join(", ")} from the environment instead of .env. ` +
+        (shadowed.length === 1
+          ? "Unset it to use the .env value."
+          : "Unset them to use the .env values."),
+    );
+}
 process.env.DO_NOT_TRACK ??= "1";
 process.env.COPILOTKIT_TELEMETRY_DISABLED ??= "true";
 
diff --git a/tests/config.test.ts b/tests/config.test.ts
index aab558a12..568eeeac7 100644
--- a/tests/config.test.ts
+++ b/tests/config.test.ts
@@ -1,6 +1,10 @@
 import assert from "node:assert/strict";
 import { test } from "node:test";
-import { assertApiDeploymentConfig, type Config } from "../apps/server/src/config.ts";
+import {
+  assertApiDeploymentConfig,
+  type Config,
+  shadowedEnvKeys,
+} from "../apps/server/src/config.ts";
 
 const sampleConfig: Config = {
   mode: "sample",
@@ -46,3 +50,10 @@ test("every API mode accepts a non-empty Intelligence key", () => {
     );
   }
 });
+
+test("environment variables that override a different .env value are reported by name", () => {
+  const file = { OPENAI_API_KEY: "sk-or-file", MODEL: "openai/gpt-5", PORT: "8787", EMPTY: "" };
+  const env = { OPENAI_API_KEY: "sk-proj-system", MODEL: "openai/gpt-5", EMPTY: "set" };
+  assert.deepEqual(shadowedEnvKeys(file, env), ["OPENAI_API_KEY", "EMPTY"]);
+  assert.deepEqual(shadowedEnvKeys(file, {}), []);
+});