diff --git a/get-shit-done/bin/lib/config.cjs b/get-shit-done/bin/lib/config.cjs
index fd1f11ae9..f36e55f19 100644
--- a/get-shit-done/bin/lib/config.cjs
+++ b/get-shit-done/bin/lib/config.cjs
@@ -440,6 +440,7 @@ function getCmdConfigSetModelProfileResultMessage(
 }
 
 module.exports = {
+  VALID_CONFIG_KEYS,
   cmdConfigEnsureSection,
   cmdConfigSet,
   cmdConfigGet,
diff --git a/get-shit-done/bin/lib/core.cjs b/get-shit-done/bin/lib/core.cjs
index 4d1f6d9fb..65b440c4f 100644
--- a/get-shit-done/bin/lib/core.cjs
+++ b/get-shit-done/bin/lib/core.cjs
@@ -286,6 +286,28 @@ function loadConfig(cwd) {
       try { fs.writeFileSync(configPath, JSON.stringify(parsed, null, 2), 'utf-8'); } catch {}
     }
 
+    // Warn about unrecognized top-level keys so users don't silently lose config.
+    // Derived from config-set's VALID_CONFIG_KEYS (canonical source) plus internal-only
+    // keys that loadConfig handles but config-set doesn't expose. This avoids maintaining
+    // a hardcoded duplicate that drifts when new config keys are added.
+    const { VALID_CONFIG_KEYS } = require('./config.cjs');
+    const KNOWN_TOP_LEVEL = new Set([
+      // Extract top-level key names from dot-notation paths (e.g., 'workflow.research' → 'workflow')
+      ...[...VALID_CONFIG_KEYS].map(k => k.split('.')[0]),
+      // Section containers that hold nested sub-keys
+      'git', 'workflow', 'planning', 'hooks',
+      // Internal keys loadConfig reads but config-set doesn't expose
+      'model_overrides', 'agent_skills', 'context_window', 'resolve_model_ids',
+      // Deprecated keys (still accepted for migration, not in config-set)
+      'depth', 'multiRepo',
+    ]);
+    const unknownKeys = Object.keys(parsed).filter(k => !KNOWN_TOP_LEVEL.has(k));
+    if (unknownKeys.length > 0) {
+      process.stderr.write(
+        `gsd-tools: warning: unknown config key(s) in .planning/config.json: ${unknownKeys.join(', ')} — these will be ignored\n`
+      );
+    }
+
     const get = (key, nested) => {
       if (parsed[key] !== undefined) return parsed[key];
       if (nested && parsed[nested.section] && parsed[nested.section][nested.field] !== undefined) {
diff --git a/tests/core.test.cjs b/tests/core.test.cjs
index 7dc61a33b..61dfad807 100644
--- a/tests/core.test.cjs
+++ b/tests/core.test.cjs
@@ -126,6 +126,61 @@ describe('loadConfig', () => {
     const config = loadConfig(tmpDir);
     assert.strictEqual(config.commit_docs, false);
   });
+
+  test('warns on unknown config keys to stderr (#1535)', () => {
+    writeConfig({ model_profile: 'quality', active_project: 'my-project', custom_flag: true });
+    const origWrite = process.stderr.write;
+    let stderrOutput = '';
+    process.stderr.write = (chunk) => { stderrOutput += chunk; };
+    try {
+      const config = loadConfig(tmpDir);
+      // Known key still loads correctly
+      assert.strictEqual(config.model_profile, 'quality');
+      // Warning emitted for unknown keys
+      assert.ok(stderrOutput.includes('active_project'), 'should warn about active_project');
+      assert.ok(stderrOutput.includes('custom_flag'), 'should warn about custom_flag');
+      assert.ok(stderrOutput.includes('ignored'), 'should mention keys will be ignored');
+    } finally {
+      process.stderr.write = origWrite;
+    }
+  });
+
+  test('known config keys are derived from VALID_CONFIG_KEYS (not hardcoded)', () => {
+    // Verify that loadConfig's unknown-key check uses config-set's VALID_CONFIG_KEYS
+    // as its source of truth. If a new key is added to config-set, it should
+    // automatically be recognized by loadConfig without a separate update.
+    const { VALID_CONFIG_KEYS } = require('../get-shit-done/bin/lib/config.cjs');
+    // Every top-level key from VALID_CONFIG_KEYS should be recognized
+    const topLevelKeys = [...VALID_CONFIG_KEYS].map(k => k.split('.')[0]);
+    for (const key of topLevelKeys) {
+      writeConfig({ [key]: 'test-value' });
+      const origWrite = process.stderr.write;
+      let stderrOutput = '';
+      process.stderr.write = (chunk) => { stderrOutput += chunk; };
+      try {
+        loadConfig(tmpDir);
+        assert.ok(
+          !stderrOutput.includes(key),
+          `VALID_CONFIG_KEYS key "${key}" should not trigger unknown-key warning`
+        );
+      } finally {
+        process.stderr.write = origWrite;
+      }
+    }
+  });
+
+  test('does not warn when all config keys are known', () => {
+    writeConfig({ model_profile: 'balanced', workflow: { research: false }, git: { branching_strategy: 'per-phase' } });
+    const origWrite = process.stderr.write;
+    let stderrOutput = '';
+    process.stderr.write = (chunk) => { stderrOutput += chunk; };
+    try {
+      loadConfig(tmpDir);
+      assert.strictEqual(stderrOutput, '', 'should not emit any warnings for valid config');
+    } finally {
+      process.stderr.write = origWrite;
+    }
+  });
 });
 
 // ─── loadConfig commit_docs gitignore auto-detection (#1250) ──────────────────