diff --git a/src/cli/doctor.ts b/src/cli/doctor.ts
index c10dc9c..c3a7930 100644
--- a/src/cli/doctor.ts
+++ b/src/cli/doctor.ts
@@ -1,6 +1,6 @@
 import type { Command } from 'commander';
 import type { Config } from '../config/index.js';
-import { getConfigPath, getDataDir, formatStatus } from './shared.js';
+import { getConfigPath, getDataDir, formatStatus, resolveOverlayPath } from './shared.js';
 import { existsSync, readFileSync, writeFileSync, unlinkSync } from 'fs';
 import { resolve, join } from 'path';
 import { parse } from 'yaml';
@@ -27,6 +27,18 @@ const checkConfigExists: Check = async (ctx) => {
   return { status: 'fail', label: 'Config file exists', detail: `not found at ${ctx.configPath}` };
 };
 
+const checkOverlayExists: Check = async (ctx) => {
+  const overlayPath = resolveOverlayPath(ctx.configPath);
+  if (!overlayPath) {
+    return { status: 'skip', label: 'Config overlay', detail: '(FLYNN_ENV not set)' };
+  }
+  const env = process.env.FLYNN_ENV;
+  if (existsSync(overlayPath)) {
+    return { status: 'pass', label: 'Config overlay', detail: `(${env}.yaml found)` };
+  }
+  return { status: 'fail', label: 'Config overlay', detail: `FLYNN_ENV=${env} but ${overlayPath} not found` };
+};
+
 const checkConfigParses: Check = async (ctx) => {
   if (!existsSync(ctx.configPath)) {
     return { status: 'skip', label: 'Config parses', detail: '(no config file)' };
@@ -203,6 +215,7 @@ const checkTailscale: Check = async (ctx) => {
 
 const allChecks: Check[] = [
   checkConfigExists,
+  checkOverlayExists,
   checkConfigParses,
   checkConfigValidates,
   checkEnvVars,