diff --git a/apps/api/src/integration-platform/controllers/sync.controller.ts b/apps/api/src/integration-platform/controllers/sync.controller.ts
index 335630d26c..93ef4e173f 100644
--- a/apps/api/src/integration-platform/controllers/sync.controller.ts
+++ b/apps/api/src/integration-platform/controllers/sync.controller.ts
@@ -1809,6 +1809,7 @@ export class SyncController {
         employees,
         options: {
           providerName: manifest.name,
+          isDirectorySource: syncDefinition.isDirectorySource ?? false,
         },
       });
 
diff --git a/apps/api/src/integration-platform/services/generic-employee-sync.service.spec.ts b/apps/api/src/integration-platform/services/generic-employee-sync.service.spec.ts
index c6c69113f1..27e1561e5b 100644
--- a/apps/api/src/integration-platform/services/generic-employee-sync.service.spec.ts
+++ b/apps/api/src/integration-platform/services/generic-employee-sync.service.spec.ts
@@ -241,4 +241,91 @@ describe('GenericEmployeeSyncService role validation', () => {
       });
     });
   });
+
+  describe('Phase 2 deactivation gating (isDirectorySource)', () => {
+    const existingOrgMember = {
+      id: 'mem_existing',
+      role: 'employee',
+      offboardDate: null,
+      user: { email: 'still-here@example.com' },
+    };
+
+    beforeEach(() => {
+      // Returned employee already has a member row → goes to Phase 1 skip path
+      mockUserFindUnique.mockResolvedValue({
+        id: 'user_returned',
+        email: 'returned@example.com',
+      });
+      mockMemberFindFirst.mockResolvedValue({
+        id: 'mem_returned',
+        role: 'employee',
+        deactivated: false,
+      });
+
+      // Phase 2 will see one other member in the same domain who was NOT returned
+      mockMemberFindMany.mockResolvedValue([existingOrgMember]);
+    });
+
+    it('skips Phase 2 by default (isDirectorySource omitted)', async () => {
+      const result = await service.processEmployees({
+        organizationId: 'org_1',
+        employees: [baseEmployee({ email: 'returned@example.com' })],
+        options: { providerName: 'Confluence' },
+      });
+
+      expect(mockMemberFindMany).not.toHaveBeenCalled();
+      expect(mockMemberUpdate).not.toHaveBeenCalled();
+      expect(result.deactivated).toBe(0);
+    });
+
+    it('skips Phase 2 when isDirectorySource is explicitly false', async () => {
+      const result = await service.processEmployees({
+        organizationId: 'org_1',
+        employees: [baseEmployee({ email: 'returned@example.com' })],
+        options: { providerName: 'Confluence', isDirectorySource: false },
+      });
+
+      expect(mockMemberFindMany).not.toHaveBeenCalled();
+      expect(mockMemberUpdate).not.toHaveBeenCalled();
+      expect(result.deactivated).toBe(0);
+    });
+
+    it('runs Phase 2 when isDirectorySource is true and deactivates absent members', async () => {
+      const result = await service.processEmployees({
+        organizationId: 'org_1',
+        employees: [baseEmployee({ email: 'returned@example.com' })],
+        options: { providerName: 'Google Workspace', isDirectorySource: true },
+      });
+
+      expect(mockMemberFindMany).toHaveBeenCalled();
+      expect(mockMemberUpdate).toHaveBeenCalledWith(
+        expect.objectContaining({
+          where: { id: 'mem_existing' },
+          data: expect.objectContaining({
+            deactivated: true,
+            isActive: false,
+          }),
+        }),
+      );
+      expect(result.deactivated).toBe(1);
+    });
+
+    it('does not deactivate when isDirectorySource is true but the absent member is in a different domain', async () => {
+      mockMemberFindMany.mockResolvedValue([
+        {
+          ...existingOrgMember,
+          user: { email: 'someone@other-domain.com' },
+        },
+      ]);
+
+      const result = await service.processEmployees({
+        organizationId: 'org_1',
+        employees: [baseEmployee({ email: 'returned@example.com' })],
+        options: { providerName: 'Google Workspace', isDirectorySource: true },
+      });
+
+      expect(mockMemberUpdate).not.toHaveBeenCalled();
+      expect(result.deactivated).toBe(0);
+    });
+  });
 });
diff --git a/apps/api/src/integration-platform/services/generic-employee-sync.service.ts b/apps/api/src/integration-platform/services/generic-employee-sync.service.ts
index 07b5fc4d0f..13608616b7 100644
--- a/apps/api/src/integration-platform/services/generic-employee-sync.service.ts
+++ b/apps/api/src/integration-platform/services/generic-employee-sync.service.ts
@@ -33,6 +33,17 @@ export interface ProcessEmployeesOptions {
   protectedRoles?: string[];
   /** Provider slug for deactivation reason messages. */
   providerName?: string;
+  /**
+   * Whether the provider is authoritative for "who works here" (directory of record).
+   *
+   * When false (default), Phase 2 is skipped entirely: members absent from the sync
+   * payload are left alone. Set true only for HRIS / identity providers whose user
+   * list = the employee list (Google Workspace, Rippling, JumpCloud, Okta, Entra).
+   *
+   * This prevents feature-licensed tools (Confluence, Slack, etc.) from silently
+   * deactivating active employees when their API returns a partial member list.
+   */
+  isDirectorySource?: boolean;
 }
 
 const DEFAULT_PROTECTED_ROLES = ['owner', 'admin', 'auditor'];
@@ -76,6 +87,7 @@ export class GenericEmployeeSyncService {
     const allowReactivation = options.allowReactivation ?? false;
     const protectedRoles = options.protectedRoles ?? DEFAULT_PROTECTED_ROLES;
     const providerName = options.providerName ?? 'provider';
+    const isDirectorySource = options.isDirectorySource ?? false;
 
     // Build the set of role identifiers we'll accept on this sync. Anything
     // outside this set is dropped (e.g. a Microsoft DSL that mis-maps
@@ -271,7 +283,20 @@ export class GenericEmployeeSyncService {
 
     // ====================================================================
     // Phase 2: Deactivate members no longer in provider
+    //
+    // Only runs when the provider is a directory of record. Feature-licensed
+    // tools (Confluence, Slack, etc.) only know who has product access — they
+    // must not be allowed to deactivate employees who didn't appear in their
+    // response, since "absent from this product" ≠ "no longer employed".
     // ====================================================================
+    if (!isDirectorySource) {
+      this.logger.log(
+        `[GenericSync] Phase 2 skipped for "${providerName}": isDirectorySource=false. Members absent from the sync payload were left alone.`,
+      );
+      results.success = results.errors === 0;
+      return results;
+    }
+
     const allOrgMembers = await db.member.findMany({
       where: {
         organizationId,
diff --git a/packages/integration-platform/src/dsl/types.ts b/packages/integration-platform/src/dsl/types.ts
index 65d1ebc6c7..36665c83fb 100644
--- a/packages/integration-platform/src/dsl/types.ts
+++ b/packages/integration-platform/src/dsl/types.ts
@@ -291,6 +291,19 @@ export const SyncDefinitionSchema = z.object({
   steps: z.array(DSLStepSchema),
   employeesPath: z.string().default('employees'),
   variables: z.array(VariableSchema).optional(),
+  /**
+   * Whether this provider is authoritative for "who works here" (directory of record).
+   *
+   * Set true ONLY for HRIS / identity providers (Google Workspace, Rippling, JumpCloud,
+   * Okta, Entra) whose user list equals the employee list. When true, the sync deactivates
+   * org members in this provider's email domain who were not returned by the sync.
+   *
+   * Default false — feature-licensed tools (Confluence, Slack, Notion, GitHub, Jira) only
+   * know "who has product access," not "who works here." Treating them as authoritative
+   * silently deactivates real employees whenever the API returns a partial list (privacy
+   * filters, scope gaps, paginated breaks, etc.).
+   */
+  isDirectorySource: z.boolean().optional().default(false),
 });
 
 export type SyncDefinition = z.infer<typeof SyncDefinitionSchema>;
diff --git a/packages/integration-platform/src/manifests/google-workspace/index.ts b/packages/integration-platform/src/manifests/google-workspace/index.ts
index 2482ba8778..0adbc65059 100644
--- a/packages/integration-platform/src/manifests/google-workspace/index.ts
+++ b/packages/integration-platform/src/manifests/google-workspace/index.ts
@@ -53,6 +53,11 @@ Note: The user authorizing must be a Google Workspace admin.`,
 
   capabilities: ['checks', 'sync'],
 
+  // Google Workspace is the customer's authoritative employee directory:
+  // users provisioned here are employees, users removed here are offboarded.
+  // Phase 2 deactivation is intentionally allowed for this provider.
+  isDirectorySource: true,
+
   services: [
     { id: 'user-sync', name: 'User Sync', description: 'Sync users from Google Workspace as organization members', enabledByDefault: true, implemented: true },
     { id: 'mfa-compliance', name: 'MFA Compliance', description: 'Monitor two-factor authentication enforcement', enabledByDefault: true, implemented: true },
diff --git a/packages/integration-platform/src/manifests/rippling/index.ts b/packages/integration-platform/src/manifests/rippling/index.ts
index 7c9a93dffa..5d773b3c6d 100644
--- a/packages/integration-platform/src/manifests/rippling/index.ts
+++ b/packages/integration-platform/src/manifests/rippling/index.ts
@@ -60,6 +60,11 @@ export const ripplingManifest: IntegrationManifest = {
   // Sync capability - this integration syncs employee data
   capabilities: ['sync'],
 
+  // Rippling is an HRIS — the authoritative source of truth for who works
+  // at the company. Phase 2 deactivation is intentionally allowed: when a
+  // worker is offboarded in Rippling they should be deactivated in Comp AI.
+  isDirectorySource: true,
+
   services: [
     { id: 'employee-sync', name: 'Employee Sync', description: 'Sync employees from Rippling to organization members', enabledByDefault: true, implemented: true },
     { id: 'device-management', name: 'Device Management', description: 'Monitor device compliance and enrollment status', implemented: false },
diff --git a/packages/integration-platform/src/types.ts b/packages/integration-platform/src/types.ts
index cf12c0e19f..9217d9d9a1 100644
--- a/packages/integration-platform/src/types.ts
+++ b/packages/integration-platform/src/types.ts
@@ -810,6 +810,21 @@ export interface IntegrationManifest {
   /** Capabilities this integration supports */
   capabilities: IntegrationCapability[];
 
+  /**
+   * Whether this integration is the authoritative source of truth for employment status.
+   *
+   * When `true`, the sync paths are allowed to deactivate members who appear in Comp AI
+   * but are absent from this provider's user list (Phase 2 deactivation).
+   *
+   * When `false` or omitted (default), Phase 2 deactivation is skipped — useful for
+   * feature-licensed tools (Confluence, Slack, Linear, etc.) whose user lists answer
+   * "who has this product" rather than "who works here."
+   *
+   * For dynamic integrations the equivalent flag lives at `syncDefinition.isDirectorySource`
+   * (see `SyncDefinitionSchema`). Code-based manifests declare it here.
+   */
+  isDirectorySource?: boolean;
+
   /**
    * Integration-level variables that are collected after authentication.
    * These can be used by checks OR by standalone features (like cloud security scanning).