diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 41fb994726..2c04b74d2a 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1332,6 +1332,15 @@ def _write_integration_json(
     )
 
 
+def _refresh_init_options_speckit_version(project_root: Path) -> None:
+    """Refresh only the Spec Kit version recorded in init-options.json."""
+    opts = load_init_options(project_root)
+    if not isinstance(opts, dict) or not opts:
+        return
+    opts["speckit_version"] = get_speckit_version()
+    save_init_options(project_root, opts)
+
+
 def _clear_init_options_for_integration(project_root: Path, integration_key: str) -> None:
     """Clear active integration keys from init-options.json when they match."""
     opts = load_init_options(project_root)
@@ -1692,6 +1701,8 @@ def integration_install(
         _write_integration_json(project_root, new_default, new_installed, settings)
         if new_default == integration.key:
             _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+        else:
+            _refresh_init_options_speckit_version(project_root)
 
     except Exception as e:
         # Attempt rollback of any files written by setup
@@ -1775,6 +1786,7 @@ def _update_init_options_for_integration(
     opts["integration"] = integration.key
     opts["ai"] = integration.key
     opts["context_file"] = integration.context_file
+    opts["speckit_version"] = get_speckit_version()
     if script_type:
         opts["script"] = script_type
     if isinstance(integration, SkillsIntegration) or getattr(integration, "_skills_mode", False):
@@ -2339,6 +2351,8 @@ def integration_upgrade(
         _write_integration_json(project_root, installed_key, installed_keys, settings)
         if installed_key == key:
             _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+        else:
+            _refresh_init_options_speckit_version(project_root)
     except Exception as exc:
         # Don't teardown — setup overwrites in-place, so teardown would
         # delete files that were working before the upgrade.  Just report.
diff --git a/tests/integrations/test_integration_subcommand.py b/tests/integrations/test_integration_subcommand.py
index abff9a5ee1..bd06f1281b 100644
--- a/tests/integrations/test_integration_subcommand.py
+++ b/tests/integrations/test_integration_subcommand.py
@@ -230,6 +230,29 @@ def test_install_multi_safe_integration(self, tmp_path):
         assert (project / ".claude" / "skills" / "speckit-plan" / "SKILL.md").exists()
         assert (project / ".agents" / "skills" / "speckit-plan" / "SKILL.md").exists()
 
+    def test_install_non_default_refreshes_init_options_version_only(self, tmp_path, monkeypatch):
+        project = _init_project(tmp_path, "claude")
+        init_options = project / ".specify" / "init-options.json"
+        opts = json.loads(init_options.read_text(encoding="utf-8"))
+        opts["speckit_version"] = "0.6.1"
+        init_options.write_text(json.dumps(opts), encoding="utf-8")
+
+        import specify_cli
+
+        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+
+        result = _run_in_project(project, [
+            "integration", "install", "codex",
+            "--script", "sh",
+        ])
+
+        assert result.exit_code == 0, result.output
+        updated = json.loads(init_options.read_text(encoding="utf-8"))
+        assert updated["speckit_version"] == "0.8.11"
+        assert updated["integration"] == "claude"
+        assert updated["ai"] == "claude"
+        assert updated["context_file"] == "CLAUDE.md"
+
     def test_install_additional_preserves_shared_manifest(self, tmp_path):
         project = _init_project(tmp_path, "claude")
         shared_manifest = project / ".specify" / "integrations" / "speckit.manifest.json"
@@ -1144,6 +1167,56 @@ def test_upgrade_invalid_manifest_reports_cli_error(self, tmp_path):
         assert "manifest" in result.output
         assert "unreadable" in result.output
 
+    def test_upgrade_refreshes_init_options_speckit_version(self, tmp_path, monkeypatch):
+        project = _init_project(tmp_path, "claude")
+        init_options = project / ".specify" / "init-options.json"
+        opts = json.loads(init_options.read_text(encoding="utf-8"))
+        opts["speckit_version"] = "0.6.1"
+        init_options.write_text(json.dumps(opts), encoding="utf-8")
+
+        import specify_cli
+
+        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+
+        result = _run_in_project(project, [
+            "integration", "upgrade", "claude",
+            "--force",
+        ])
+
+        assert result.exit_code == 0, result.output
+        updated = json.loads(init_options.read_text(encoding="utf-8"))
+        assert updated["speckit_version"] == "0.8.11"
+
+    def test_upgrade_non_default_refreshes_init_options_version_only(self, tmp_path, monkeypatch):
+        project = _init_project(tmp_path, "gemini")
+        install = _run_in_project(project, [
+            "integration", "install", "claude",
+            "--script", "sh",
+        ])
+        assert install.exit_code == 0, install.output
+
+        init_options = project / ".specify" / "init-options.json"
+        opts = json.loads(init_options.read_text(encoding="utf-8"))
+        opts["speckit_version"] = "0.6.1"
+        init_options.write_text(json.dumps(opts), encoding="utf-8")
+
+        import specify_cli
+
+        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+
+        result = _run_in_project(project, [
+            "integration", "upgrade", "claude",
+            "--script", "sh",
+            "--force",
+        ])
+
+        assert result.exit_code == 0, result.output
+        updated = json.loads(init_options.read_text(encoding="utf-8"))
+        assert updated["speckit_version"] == "0.8.11"
+        assert updated["integration"] == "gemini"
+        assert updated["ai"] == "gemini"
+        assert updated["context_file"] == "GEMINI.md"
+
     def test_upgrade_does_not_persist_state_when_template_refresh_fails(self, tmp_path, monkeypatch):
         project = _init_project(tmp_path, "claude")
         int_json = project / ".specify" / "integration.json"