diff --git a/backend/.sqlx/query-255ba68caa78d0e814ea817693a319f769907025f9c7d1150d45e8ecb1bff4ab.json b/backend/.sqlx/query-255ba68caa78d0e814ea817693a319f769907025f9c7d1150d45e8ecb1bff4ab.json
deleted file mode 100644
index 245c65a7a8..0000000000
--- a/backend/.sqlx/query-255ba68caa78d0e814ea817693a319f769907025f9c7d1150d45e8ecb1bff4ab.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
-  "db_name": "PostgreSQL",
-  "query": "UPDATE workspace_settings SET auto_invite = $1 WHERE workspace_id = $2",
-  "describe": {
-    "columns": [],
-    "parameters": {
-      "Left": [
-        "Jsonb",
-        "Text"
-      ]
-    },
-    "nullable": []
-  },
-  "hash": "255ba68caa78d0e814ea817693a319f769907025f9c7d1150d45e8ecb1bff4ab"
-}
diff --git a/backend/.sqlx/query-a1bcf143135ecb9f32709a56a353d3246dc238920c3e155caa9cf767246fa6fb.json b/backend/.sqlx/query-a1bcf143135ecb9f32709a56a353d3246dc238920c3e155caa9cf767246fa6fb.json
new file mode 100644
index 0000000000..18ee22083e
--- /dev/null
+++ b/backend/.sqlx/query-a1bcf143135ecb9f32709a56a353d3246dc238920c3e155caa9cf767246fa6fb.json
@@ -0,0 +1,15 @@
+{
+  "db_name": "PostgreSQL",
+  "query": "UPDATE workspace_settings SET auto_invite = (COALESCE(auto_invite, '{}'::jsonb) - 'domain') || $1::jsonb WHERE workspace_id = $2",
+  "describe": {
+    "columns": [],
+    "parameters": {
+      "Left": [
+        "Jsonb",
+        "Text"
+      ]
+    },
+    "nullable": []
+  },
+  "hash": "a1bcf143135ecb9f32709a56a353d3246dc238920c3e155caa9cf767246fa6fb"
+}
diff --git a/backend/ee-repo-ref.txt b/backend/ee-repo-ref.txt
index cc50737a1d..3d9d49412a 100644
--- a/backend/ee-repo-ref.txt
+++ b/backend/ee-repo-ref.txt
@@ -1 +1 @@
-7e338e4dabf91689bfd7fb0333c6534040b17b59
+f2fced19fcae81de7f6dac545010ce404c052e1b
diff --git a/backend/windmill-api-integration-tests/tests/workspaces.rs b/backend/windmill-api-integration-tests/tests/workspaces.rs
index 25312cae27..ff603269e7 100644
--- a/backend/windmill-api-integration-tests/tests/workspaces.rs
+++ b/backend/windmill-api-integration-tests/tests/workspaces.rs
@@ -1166,3 +1166,47 @@ async fn test_create_service_account_drops_orphaned_group_memberships(
 
     Ok(())
 }
+
+#[cfg(feature = "private")]
+#[sqlx::test(migrations = "../migrations", fixtures("base"))]
+async fn test_edit_auto_invite_preserves_instance_groups(db: Pool<Postgres>) -> anyhow::Result<()> {
+    initialize_tracing().await;
+
+    sqlx::query(
+        r#"UPDATE workspace_settings
+           SET auto_invite = '{"instance_groups": ["eng"], "instance_groups_roles": {"eng": "developer"}}'
+           WHERE workspace_id = 'test-workspace'"#,
+    )
+    .execute(&db)
+    .await?;
+
+    let server = ApiServer::start(db.clone()).await?;
+    let port = server.addr.port();
+    let base = format!("http://localhost:{port}/api/w/test-workspace/workspaces");
+
+    // enable, then disable
+    for body in [
+        json!({"operator": false, "invite_all": true, "auto_add": false}),
+        json!({}),
+    ] {
+        let resp = authed(client().post(format!("{base}/edit_auto_invite")))
+            .json(&body)
+            .send()
+            .await?;
+        assert_eq!(resp.status(), 200, "{body}: {}", resp.text().await?);
+
+        let auto_invite: serde_json::Value = sqlx::query_scalar(
+            "SELECT auto_invite FROM workspace_settings WHERE workspace_id = 'test-workspace'",
+        )
+        .fetch_one(&db)
+        .await?;
+        assert_eq!(auto_invite["instance_groups"], json!(["eng"]), "{body}");
+        assert_eq!(
+            auto_invite["instance_groups_roles"],
+            json!({"eng": "developer"}),
+            "{body}"
+        );
+    }
+
+    Ok(())
+}
diff --git a/cli/src/commands/sync/sync.ts b/cli/src/commands/sync/sync.ts
index 138a346594..6040afc747 100644
--- a/cli/src/commands/sync/sync.ts
+++ b/cli/src/commands/sync/sync.ts
@@ -2546,9 +2546,9 @@ export function preservePendingScriptLocks(
 }
 
 // `sync push` never applies the workspace's display name from settings.yaml and
-// applies its color only when the local file carries one (see
-// pushWorkspaceSettings), so on a push the fields it would not apply must
-// compare equal, or the row is listed on every run.
+// applies its color and auto_invite.instance_groups only when the local file
+// carries them (see pushWorkspaceSettings), so on a push the fields it would not
+// apply must compare equal, or the row is listed on every run.
 const isWorkspaceSettingsFile = (p: string) =>
   /^settings(\.[^./\\]+)?\.(yaml|json)$/.test(p);
 function stripUnappliedSettingsFields(local: any, remote: any) {
@@ -2558,6 +2558,20 @@ function stripUnappliedSettingsFields(local: any, remote: any) {
     delete local?.color;
     delete remote?.color;
   }
+  // push reads a missing auto_invite as {} on both sides
+  if (local) local.auto_invite ??= {};
+  if (remote) remote.auto_invite ??= {};
+  const localInvite = local?.auto_invite;
+  const remoteInvite = remote?.auto_invite;
+  if (localInvite?.instance_groups == null) {
+    for (const invite of [localInvite, remoteInvite]) {
+      delete invite?.instance_groups;
+      delete invite?.instance_groups_roles;
+    }
+  } else {
+    localInvite.instance_groups_roles ??= {};
+    if (remoteInvite) remoteInvite.instance_groups_roles ??= {};
+  }
 }
 
 export async function compareDynFSElement(
diff --git a/cli/src/core/settings.ts b/cli/src/core/settings.ts
index 4174ec0358..6a9358b468 100644
--- a/cli/src/core/settings.ts
+++ b/cli/src/core/settings.ts
@@ -239,8 +239,19 @@ export async function pushWorkspaceSettings(
     });
   }
 
-  // Handle auto_invite using grouped format
-  if (!deepEqual(localSettings.auto_invite, settings.auto_invite)) {
+  // Handle auto_invite using grouped format. The domain invite and the instance groups
+  // are applied by separate endpoints, each rewriting only its own keys.
+  const {
+    instance_groups: localGroups,
+    instance_groups_roles: localGroupRoles,
+    ...localDomainInvite
+  } = localSettings.auto_invite ?? {};
+  const {
+    instance_groups: remoteGroups,
+    instance_groups_roles: remoteGroupRoles,
+    ...remoteDomainInvite
+  } = settings.auto_invite ?? {};
+  if (!deepEqual(localDomainInvite, remoteDomainInvite)) {
     log.debug(`Updating auto invite...`);
 
     const localAutoInvite = localSettings.auto_invite;
@@ -278,6 +289,20 @@ export async function pushWorkspaceSettings(
     }
   }
 
+  // Only when settings.yaml declares instance_groups: clearing a group removes the
+  // workspace members it granted, so an absent key must never clear it.
+  if (
+    localGroups != undefined &&
+    (!deepEqual(localGroups, remoteGroups) ||
+      !deepEqual(localGroupRoles ?? {}, remoteGroupRoles ?? {}))
+  ) {
+    log.debug(`Updating instance groups...`);
+    await wmill.editInstanceGroups({
+      workspace,
+      requestBody: { groups: localGroups, roles: localGroupRoles ?? {} },
+    });
+  }
+
   if (!deepEqual(localSettings.ai_config, settings.ai_config)) {
     log.debug(`Updating copilot settings...`);
     await wmill.editCopilotConfig({
diff --git a/cli/test/push_diff_convergence_unit.test.ts b/cli/test/push_diff_convergence_unit.test.ts
index 67f6d5b4dd..a6f2c132c0 100644
--- a/cli/test/push_diff_convergence_unit.test.ts
+++ b/cli/test/push_diff_convergence_unit.test.ts
@@ -320,3 +320,29 @@ test("push: settings.yaml differing only by name or an unset color is not a chan
   });
   expect(await diff(otherColor, remote, skips)).toEqual(["edited settings.yaml"]);
 });
+
+// A push applies auto_invite.instance_groups only when the local file declares
+// them (see pushWorkspaceSettings).
+test("push: settings.yaml without instance_groups is not a change", async () => {
+  const remote = local({
+    "settings.yaml":
+      "name: prod\nauto_invite:\n  enabled: false\n  instance_groups:\n    - eng\n  instance_groups_roles:\n    eng: developer\n",
+  });
+  const undeclared = local({
+    "settings.yaml": "name: prod\nauto_invite:\n  enabled: false\n",
+  });
+  const skips = { includeSettings: true };
+  expect(await diff(undeclared, remote, skips)).toEqual([]);
+
+  const groupsOnlyRemote = local({
+    "settings.yaml": "name: prod\nauto_invite:\n  instance_groups:\n    - eng\n",
+  });
+  const noAutoInvite = local({ "settings.yaml": "name: prod\n" });
+  expect(await diff(noAutoInvite, groupsOnlyRemote, skips)).toEqual([]);
+
+  const otherGroups = local({
+    "settings.yaml":
+      "name: prod\nauto_invite:\n  enabled: false\n  instance_groups: []\n",
+  });
+  expect(await diff(otherGroups, remote, skips)).toEqual(["edited settings.yaml"]);
+});
diff --git a/cli/test/push_workspace_settings_auto_invite_unit.test.ts b/cli/test/push_workspace_settings_auto_invite_unit.test.ts
new file mode 100644
index 0000000000..b04d895056
--- /dev/null
+++ b/cli/test/push_workspace_settings_auto_invite_unit.test.ts
@@ -0,0 +1,82 @@
+/**
+ * Regression guard: `sync push` (pushWorkspaceSettings) applies the domain invite and
+ * the instance groups of `auto_invite` through their own endpoints, and never clears
+ * instance groups that settings.yaml does not declare.
+ */
+
+import { expect, test, describe, beforeEach, mock } from "bun:test";
+
+let editAutoInviteCalls: unknown[] = [];
+let editInstanceGroupsCalls: unknown[] = [];
+const remoteAutoInvite = {
+  enabled: true,
+  domain: "*",
+  operator: false,
+  mode: "invite",
+  instance_groups: ["eng"],
+  instance_groups_roles: { eng: "developer" },
+};
+
+// Every wmill.* call reachable from pushWorkspaceSettings is stubbed: bun shares one
+// mocked module across test files, and names missing from whichever mock loads first
+// stay missing for the others.
+mock.module("../gen/services.gen.ts", () => ({
+  getSettings: async () => ({ auto_invite: remoteAutoInvite }),
+  getWorkspaceName: async () => "phoenix",
+  changeWorkspaceName: async () => {},
+  changeWorkspaceColor: async () => {},
+  editWebhook: async () => {},
+  editAutoInvite: async (a: unknown) => {
+    editAutoInviteCalls.push(a);
+  },
+  editInstanceGroups: async (a: unknown) => {
+    editInstanceGroupsCalls.push(a);
+  },
+  editErrorHandler: async () => {},
+  editSuccessHandler: async () => {},
+  editCopilotConfig: async () => {},
+  editLargeFileStorageConfig: async () => {},
+  editWorkspaceGitSyncConfig: async () => {},
+  editWorkspaceDefaultApp: async () => {},
+  editDefaultScripts: async () => {},
+  workspaceMuteCriticalAlertsUi: async () => {},
+  updateOperatorSettings: async () => {},
+  editDataTableConfig: async () => {},
+  editSlackCommand: async () => {},
+  setWorkspaceSlackOauthConfig: async () => {},
+  deleteWorkspaceSlackOauthConfig: async () => {},
+}));
+
+const { pushWorkspaceSettings } = await import("../src/core/settings.ts");
+
+describe("pushWorkspaceSettings auto_invite", () => {
+  beforeEach(() => {
+    editAutoInviteCalls = [];
+    editInstanceGroupsCalls = [];
+  });
+
+  test("an instance-group-only change updates the groups and leaves the domain invite", async () => {
+    await pushWorkspaceSettings("phoenix", "settings", undefined, {
+      name: "phoenix",
+      auto_invite: { ...remoteAutoInvite, instance_groups_roles: { eng: "admin" } },
+    });
+    expect(editAutoInviteCalls.length).toBe(0);
+    expect(editInstanceGroupsCalls).toEqual([
+      {
+        workspace: "phoenix",
+        requestBody: { groups: ["eng"], roles: { eng: "admin" } },
+      },
+    ]);
+  });
+
+  test("a settings.yaml without instance_groups does not clear them", async () => {
+    const { instance_groups: _g, instance_groups_roles: _r, ...domainInvite } =
+      remoteAutoInvite;
+    await pushWorkspaceSettings("phoenix", "settings", undefined, {
+      name: "phoenix",
+      auto_invite: { ...domainInvite, operator: true },
+    });
+    expect(editAutoInviteCalls.length).toBe(1);
+    expect(editInstanceGroupsCalls.length).toBe(0);
+  });
+});
diff --git a/cli/test/push_workspace_settings_identity_unit.test.ts b/cli/test/push_workspace_settings_identity_unit.test.ts
index c583a53282..5dcf9815ef 100644
--- a/cli/test/push_workspace_settings_identity_unit.test.ts
+++ b/cli/test/push_workspace_settings_identity_unit.test.ts
@@ -31,6 +31,7 @@ mock.module("../gen/services.gen.ts", () => ({
     editWebhookCalls.push(a);
   },
   editAutoInvite: async () => {},
+  editInstanceGroups: async () => {},
   editErrorHandler: async () => {},
   editSuccessHandler: async () => {},
   editCopilotConfig: async () => {},