diff --git a/src/cli.ts b/src/cli.ts
index 28e7e12d6..b14d5b1f1 100644
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -298,6 +298,10 @@ if (cliFlags.messages[0] === 'sessions') {
 // `gsd headless` — run auto-mode without TUI
 if (cliFlags.messages[0] === 'headless') {
   await ensureRtkBootstrap()
+  // Sync bundled resources before headless runs (#3471). Without this,
+  // headless-query loads from src/resources/ while auto/interactive load
+  // from ~/.gsd/agent/extensions/ — different extension copies diverge.
+  initResources(agentDir)
   const { runHeadless, parseHeadlessArgs } = await import('./headless.js')
   await runHeadless(parseHeadlessArgs(process.argv))
   process.exit(0)
diff --git a/src/headless-query.ts b/src/headless-query.ts
index c9aa6ae2b..cc7c134c3 100644
--- a/src/headless-query.ts
+++ b/src/headless-query.ts
@@ -16,12 +16,22 @@
 
 import { createJiti } from '@mariozechner/jiti'
 import { fileURLToPath } from 'node:url'
+import { join } from 'node:path'
+import { homedir } from 'node:os'
 import type { GSDState } from './resources/extensions/gsd/types.js'
 import { resolveBundledSourceResource } from './bundled-resource-path.js'
 
 const jiti = createJiti(fileURLToPath(import.meta.url), { interopDefault: true, debug: false })
+// Resolve extensions from the synced agent directory so headless-query
+// loads the same extension copy as interactive/auto modes (#3471).
+// Falls back to bundled source for source-tree dev workflows.
+const agentExtensionsDir = join(process.env.GSD_AGENT_DIR || join(homedir(), '.gsd', 'agent'), 'extensions', 'gsd')
+const { existsSync } = await import('node:fs')
+const useAgentDir = existsSync(join(agentExtensionsDir, 'state.ts'))
 const gsdExtensionPath = (...segments: string[]) =>
-  resolveBundledSourceResource(import.meta.url, 'extensions', 'gsd', ...segments)
+  useAgentDir
+    ? join(agentExtensionsDir, ...segments)
+    : resolveBundledSourceResource(import.meta.url, 'extensions', 'gsd', ...segments)
 
 async function loadExtensionModules() {
   const stateModule = await jiti.import(gsdExtensionPath('state.ts'), {}) as any
diff --git a/src/tests/headless-query-extension-path.test.ts b/src/tests/headless-query-extension-path.test.ts
new file mode 100644
index 000000000..499509187
--- /dev/null
+++ b/src/tests/headless-query-extension-path.test.ts
@@ -0,0 +1,28 @@
+/**
+ * Regression test for #3471: headless-query must load extensions from
+ * the synced agent directory, not directly from src/resources/.
+ */
+import { test } from "node:test";
+import assert from "node:assert/strict";
+import { readFileSync } from "node:fs";
+import { join, dirname } from "node:path";
+import { fileURLToPath } from "node:url";
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+
+test("headless-query resolves from agent extensions dir (#3471)", () => {
+  const src = readFileSync(join(__dirname, "..", "headless-query.ts"), "utf-8");
+  assert.ok(
+    src.includes("agentExtensionsDir") || src.includes(".gsd/agent"),
+    "headless-query must resolve from synced agent directory",
+  );
+});
+
+test("cli.ts calls initResources before headless (#3471)", () => {
+  const src = readFileSync(join(__dirname, "..", "cli.ts"), "utf-8");
+  const headlessBlock = src.slice(src.indexOf("gsd headless"));
+  const initIdx = headlessBlock.indexOf("initResources");
+  const runIdx = headlessBlock.indexOf("runHeadless");
+  assert.ok(initIdx !== -1, "initResources must be called before headless");
+  assert.ok(initIdx < runIdx, "initResources must come before runHeadless");
+});