diff --git a/packages/app/src/cli/api/graphql/business-platform-organizations/generated/types.d.ts b/packages/app/src/cli/api/graphql/business-platform-organizations/generated/types.d.ts
index 200b94d9837..e6d67fd75a1 100644
--- a/packages/app/src/cli/api/graphql/business-platform-organizations/generated/types.d.ts
+++ b/packages/app/src/cli/api/graphql/business-platform-organizations/generated/types.d.ts
@@ -80,13 +80,16 @@ export type Scalars = {
   URL: { input: string; output: string; }
 };
 
-/** Operators for user filter queries. */
+/** Operators for filter queries. */
 export type Operator =
   /** Between operator. */
   | 'BETWEEN'
   /** Equals operator. */
   | 'EQUALS'
-  /** In operator. */
+  /**
+   * In operator. Accepts a comma-separated string of values (e.g.
+   * "value1,value2,value3"). Not supported for all filter fields.
+   */
   | 'IN';
 
 export type OrganizationUserProvisionShopAccessInput = {
@@ -113,17 +116,23 @@ export type ShopFilterField =
    * `inactive`, `cancelled`, `client_transfer`, `plus_client_transfer`,
    * `development_legacy`, `custom`, `fraudulent`, `staff`, `trial`,
    * `plus_development`, `retail`, `shop_pay_commerce_components`, `non_profit`.
+   * With the `In` operator, use raw plan names (e.g. "professional,shopify_plus").
    */
   | 'SHOP_PLAN'
   /** The active/inactive status of the shop. Values: `active`, `inactive`. */
   | 'STORE_STATUS'
   /**
-   * The type of the shop. Values: `development`, `production`, `app_development`,
-   * `development_superset`, `client_transfer`, `collaborator`.
+   * The type of the shop. Does not support the `In` operator. Values:
+   * `development`, `production`, `app_development`, `development_superset`,
+   * `client_transfer`, `collaborator`.
    */
   | 'STORE_TYPE';
 
-/** Represents a single filter option for shop queries. */
+/**
+ * Represents a single filter option for shop queries. When using the `In`
+ * operator, pass a comma-separated string of values (e.g. "value1,value2").
+ * Maximum 20 values.
+ */
 export type ShopFilterInput = {
   field: ShopFilterField;
   operator: Operator;
diff --git a/packages/cli/src/cli/services/store/auth/index.test.ts b/packages/cli/src/cli/services/store/auth/index.test.ts
index 89df34ba6db..e3dc4be55c5 100644
--- a/packages/cli/src/cli/services/store/auth/index.test.ts
+++ b/packages/cli/src/cli/services/store/auth/index.test.ts
@@ -306,6 +306,42 @@ describe('store auth service', () => {
     expect(setStoredStoreAppSession).not.toHaveBeenCalled()
   })
 
+  test('authenticateStoreWithApp succeeds when scopes input is space-separated', async () => {
+    const waitForStoreAuthCodeMock = vi.fn().mockImplementation(async (options) => {
+      await options.onListening?.()
+      return 'abc123'
+    })
+
+    const result = await authenticateStoreWithApp(
+      {
+        store: 'shop.myshopify.com',
+        scopes: 'read_products read_inventory',
+      },
+      {
+        openURL: vi.fn().mockResolvedValue(true),
+        waitForStoreAuthCode: waitForStoreAuthCodeMock,
+        exchangeStoreAuthCodeForToken: vi.fn().mockResolvedValue({
+          access_token: 'token',
+          scope: 'read_products,read_inventory',
+          expires_in: 86400,
+          associated_user: {id: 42, email: 'test@example.com'},
+        }),
+        presenter: {
+          openingBrowser: vi.fn(),
+          manualAuthUrl: vi.fn(),
+          success: vi.fn(),
+        },
+      },
+    )
+
+    expect(result.scopes).toEqual(['read_products', 'read_inventory'])
+    expect(setStoredStoreAppSession).toHaveBeenCalledWith(
+      expect.objectContaining({
+        scopes: ['read_products', 'read_inventory'],
+      }),
+    )
+  })
+
   test('authenticateStoreWithApp accepts compressed write scopes that imply requested read scopes', async () => {
     const waitForStoreAuthCodeMock = vi.fn().mockImplementation(async (options) => {
       await options.onListening?.()
diff --git a/packages/cli/src/cli/services/store/auth/scopes.test.ts b/packages/cli/src/cli/services/store/auth/scopes.test.ts
index 5dbb0dba04f..c157d5f00a6 100644
--- a/packages/cli/src/cli/services/store/auth/scopes.test.ts
+++ b/packages/cli/src/cli/services/store/auth/scopes.test.ts
@@ -17,6 +17,30 @@ describe('store auth scope helpers', () => {
     expect(mergeRequestedAndStoredScopes(['read_products'], ['read_orders'])).toEqual(['read_orders', 'read_products'])
   })
 
+  test('parseStoreAuthScopes splits space-separated scopes', () => {
+    expect(parseStoreAuthScopes('read_products read_inventory')).toEqual(['read_products', 'read_inventory'])
+  })
+
+  test('parseStoreAuthScopes splits mixed comma-and-space delimiters', () => {
+    expect(parseStoreAuthScopes('read_products, read_inventory,write_orders')).toEqual([
+      'read_products',
+      'read_inventory',
+      'write_orders',
+    ])
+  })
+
+  test('resolveGrantedScopes succeeds when granted scopes are space-separated', () => {
+    expect(
+      resolveGrantedScopes(
+        {
+          access_token: 'token',
+          scope: 'read_products read_inventory',
+        },
+        ['read_products', 'read_inventory'],
+      ),
+    ).toEqual(['read_products', 'read_inventory'])
+  })
+
   test('resolveGrantedScopes accepts compressed write scopes that imply requested reads', () => {
     expect(
       resolveGrantedScopes(
diff --git a/packages/cli/src/cli/services/store/auth/scopes.ts b/packages/cli/src/cli/services/store/auth/scopes.ts
index efe8a2b5913..ea3225934a7 100644
--- a/packages/cli/src/cli/services/store/auth/scopes.ts
+++ b/packages/cli/src/cli/services/store/auth/scopes.ts
@@ -3,10 +3,7 @@ import {outputContent, outputDebug} from '@shopify/cli-kit/node/output'
 import type {StoreTokenResponse} from './token-client.js'
 
 export function parseStoreAuthScopes(input: string): string[] {
-  const scopes = input
-    .split(',')
-    .map((scope) => scope.trim())
-    .filter(Boolean)
+  const scopes = input.split(/[ ,]+/).filter(Boolean)
 
   if (scopes.length === 0) {
     throw new AbortError('At least one scope is required.', 'Pass --scopes as a comma-separated list.')