diff --git a/src/apm_cli/integration/hook_integrator.py b/src/apm_cli/integration/hook_integrator.py
index 412a60f74..5b0d96657 100644
--- a/src/apm_cli/integration/hook_integrator.py
+++ b/src/apm_cli/integration/hook_integrator.py
@@ -1283,6 +1283,8 @@ def integrate_package_hooks(
                     renamed_hooks[event_name] = entries
                 rewritten["hooks"] = renamed_hooks
 
+            rewritten.setdefault("version", 1)
+
             # Write rewritten JSON
             with open(target_path, "w", encoding="utf-8") as f:
                 json.dump(rewritten, f, indent=2)
diff --git a/tests/integration/test_hook_integrator_copilot_casing_e2e.py b/tests/integration/test_hook_integrator_copilot_casing_e2e.py
index 8fcf85fba..0f995f741 100644
--- a/tests/integration/test_hook_integrator_copilot_casing_e2e.py
+++ b/tests/integration/test_hook_integrator_copilot_casing_e2e.py
@@ -80,7 +80,9 @@ def _read_copilot_hooks_config(project_root: Path, package_name: str) -> dict[st
     """Read the actual Copilot hook JSON written under .github/hooks."""
     config_path = project_root / ".github" / "hooks" / f"{package_name}-hooks.json"
     assert config_path.exists()
-    return json.loads(config_path.read_text(encoding="utf-8"))
+    config = json.loads(config_path.read_text(encoding="utf-8"))
+    assert config["version"] == 1
+    return config
 
 
 def test_copilot_install_writes_only_camel_case_hook_events(tmp_path: Path) -> None:
diff --git a/tests/unit/integration/test_hook_integrator.py b/tests/unit/integration/test_hook_integrator.py
index 558496358..023bdfb50 100644
--- a/tests/unit/integration/test_hook_integrator.py
+++ b/tests/unit/integration/test_hook_integrator.py
@@ -281,6 +281,32 @@ def test_integrate_hookify_vscode(self, temp_project):
         assert (scripts_dir / "stop.py").exists()
         assert (scripts_dir / "userpromptsubmit.py").exists()
 
+    def test_copilot_version_emitted_on_fresh_install(self, temp_project):
+        """Fresh Copilot hook JSON must contain top-level "version": 1."""
+        pkg_info = self._setup_hookify_package(temp_project)
+        integrator = HookIntegrator()
+
+        integrator.integrate_package_hooks(pkg_info, temp_project)
+
+        hooks_path = temp_project / ".github" / "hooks" / "hookify-hooks.json"
+        config = json.loads(hooks_path.read_text())
+        assert config["version"] == 1
+
+    def test_copilot_existing_source_version_preserved(self, temp_project):
+        """An explicit source version must not be overwritten."""
+        pkg_info = self._setup_hookify_package(temp_project)
+        source_path = pkg_info.install_path / "hooks" / "hooks.json"
+        source_config = json.loads(source_path.read_text())
+        source_config["version"] = 3
+        source_path.write_text(json.dumps(source_config))
+
+        integrator = HookIntegrator()
+        integrator.integrate_package_hooks(pkg_info, temp_project)
+
+        hooks_path = temp_project / ".github" / "hooks" / "hookify-hooks.json"
+        config = json.loads(hooks_path.read_text())
+        assert config["version"] == 3
+
     def test_integrate_learning_output_style_vscode(self, temp_project):
         """Test VSCode integration of learning-output-style plugin (different script dir)."""
         pkg_dir = temp_project / "apm_modules" / "anthropics" / "learning-output-style"