Atlassian Organization consolidation guide

Summary

Organization consolidation (sometimes called an organization migration) transfers all products, sites, and users from one organization (the source) into another (the destination). Because the process is managed primarily by Atlassian and involves multiple phases, this guide will help you prepare, set expectations, and understand the end-to-end timeline.

Note: Consolidations are performed only for both Organizations on the Centralized User Management. If your organization is on the Original User Management, you will need to follow the steps to transfer all products to another organization.

Section 1: Understanding Atlassian Organizations

An Atlassian Organization is your company-wide administration layer. You get one when you sign up for an Atlassian product or create an organization without products.

Organizations currently operate under one of two user management experiences:

Note: The user management experience may look different depending on your organization's setup. See Original user management: See all the users and groups in your organization for details on recent changes.

Section 2: Should You Consolidate?

Before starting, determine whether consolidation is right for you. Review Can I merge my Atlassian organizations? to understand:

• Whether it's technically possible to merge your organizations

• Whether you already have centralized user management

• Whether you have an Atlassian Guard subscription

• The benefits and trade-offs of consolidating

Whether moving only selected products is a better option

Section 3: What to Know Before Requesting Consolidation

Consolidation is a significant, irreversible process. Review Transfer all apps to another organization (this page is only for organizations on the Original user management, but has some useful information) alongside these key points:

How it works:

• Sites, products, and users are merged from the source into the destination organization. The source organization ID is deactivated after the consolidation is completed.

• To begin the assessment, please share your source and destination organization IDs. You can find these by following the steps in Retrieve my Atlassian Cloud Organization's ID.

• The Site URLs or Apps present on the source organization are not changed or affected during the consolidation process.

• A consolidation will unlink all apps and sites associated with the source organization and relink them to the destination organization as-is.

• Source organization admins become organization admins in the destination. If org admin groups have product access, this may cause a license limit breach.

• The process is not reversible. After consolidation, you can't split the destination organization back into the two original organizations.

User status considerations:

• If the same user account is active in one organization and inactive in the other, the user will be inactive in the merged organization, potentially losing access to products.

• To avoid this, we remove the user from products in the organization where they are inactive before the merge, then reactivate them. We’ll share a list of users with this status mismatch between organizations when sharing the preflight checks.

Groups:

• Groups with the same name in both organizations will be renamed in the source using the format: {groupName}-{SourceOrgName}.

• The admin group (org-admins or site-admins) from the source will be renamed to legacy-org-admins-{SecondaryOrgName} and will no longer grant administrative permissions.

Identity Provider (IDP) behavior after consolidation:

After consolidation, all IDPs are managed by the destination organization and will provision users across all sites, including those that were previously part of the source organization. This means any users managed by your IDP may automatically gain access to sites they did not previously belong to.

If your organization manages multiple separate legal entities, this behavior can create compliance risks:

• Data residency: Users from one entity may be granted access to sites where data is stored in a different region, potentially violating your data residency commitments.

• GDPR / privacy: Employees from one legal entity may gain visibility into data (such as Jira projects or Confluence spaces) belonging to a different entity, which may not be permitted under your internal data processing agreements or applicable privacy laws.

• Access control: Groups synced via SCIM may include users from across entities, leading to unintended access to sensitive content.

Recommendation: Before proceeding with consolidation, review your IDP and SCIM group configurations and assess whether all sites should be accessible to all IDP-managed users.

Timing and availability:

• During consolidation, the admin hub for both organizations will be in read-only mode. You can't add users, create groups, or invite users during this time.

• Site and product changes are blocked during the consolidation window. You will not be able to create or remove sites, or activate new Atlassian apps. Any attempt to do so will result in an error — this is expected. We recommend not making any changes to your sites or product subscriptions until the consolidation is complete.

• Phase 1: Userbase Merge All user accounts, groups, and group memberships from the source organization are merged into the destination organization. After this phase, all users are managed under a single organization and can access products across both the source and destination sites. The administrative consolidation (userbase merge) typically completes in approximately 1–4 hours, depending on the size of the userbase.

• Phase 2: Teamwork Graph Merge Teamwork Graph is Atlassian's cross-product data layer that powers features like search, notifications, recent activity, and user mentions across Jira, Confluence, and other Atlassian products. During this phase, the cross-product data from the source organization is merged into the destination so that these features work seamlessly across all sites. For most organizations, this completes within 1 hour. For exceptionally large organizations, this may take longer — the total consolidation window, including both phases, could take 4–6 hours or more.

• Consolidations are executed on Tuesdays, Wednesdays, Thursdays, or Fridays between 9:00 a.m. and 12:00 p.m. Sydney (Australia) time.

• If you are consolidating more than two organizations sequentially (into the same destination), there must be a minimum 48-hour cooldown period between each consolidation.

Section 4: Licensing, Billing, and Marketplace Apps

Important: Organization consolidation is an administrative change that merges users, groups, and sites into a single organization. It is not a billing change. Billing and licensing for the sites transferred from the source organization are not automatically updated during the consolidation. After the consolidation, you will need to manually align your subscriptions to the destination billing accounts and plans.

Licensing After Consolidation

User-based licensing:

• Organization admins from the source organization will become organization admins in the destination, which may grant them product access they didn't previously have, potentially increasing your license consumption. Review org-admin group memberships before the merge to avoid unexpected license breaches.

Plan tier alignment:

• If both your source and destination organizations have an enterprise plan, only one organization can retain an enterprise entitlement. The source organization must be downgraded to Premium before the merge. After the consolidation is complete, the sites from the source organization can be linked to the destination organization's enterprise plan.

Enterprise licensing after the consolidation:

• After the consolidation is complete, the sites transferred from the source organization will not automatically be upgraded to enterprise — even if the destination organization is on the enterprise plan.

• To upgrade these sites to enterprise and avoid separate billing for users, contact our Deal Desk Support team. To start this process, send an email to sales-ops-support@atlassian.com, and a new ticket will be created automatically on your behalf.

• Any licensing and billing questions or adjustments post-consolidation can be addressed through this team.

Marketplace Apps

Marketplace app subscriptions are licensed per site and per host product (for example, a Jira plugin on Site A is a separate subscription from the same plugin on Site B). Organization consolidation does not automatically migrate, merge, or de-duplicate app subscriptions. Here's what to expect:

• Apps stay on their sites. Apps installed on each site will continue to function on their respective site after consolidation. No app data is moved or merged during the consolidation process.

Marketplace apps are not affected. Organization consolidation does not change, merge, or modify Marketplace app subscriptions or billing. If both organizations had the same app installed, you would have multiple app instances after the consolidation; each would remain on its respective site with its own separate billing.

Section 5: Pre-Consolidation Requirements

The following requirements must be met before the consolidation can proceed. Atlassian Support will validate these, but being prepared will reduce back-and-forth:

• Both organizations must be on centralized user management.

• Both organizations must share one common organization admin.

• No Atlassian Support accounts should be present in either organization (e.g., from consent granted through support tickets).

• The source organization must not have any siteless products (e.g., Trello or Bitbucket workspaces). These need to be transferred or migrated beforehand.

• The total number of users, groups, and group memberships must be fewer than 500,000.

• User Access Settings in the source organization must be reset. Refer: How to Reset App Access Settings Before a Product Transfer.

• No users should have a conflicting status across both organizations (e.g., active in one and inactive in the other).

Section 6: The Consolidation Process - Phase by Phase

Phase 1: Information Gathering

• Atlassian Support will confirm details about both organizations, including what is highlighted in “Can I merge my Atlassian organizations?” and “Transfer all apps to another organization.”

Phase 2: Migrating to Centralized User Management

• If the source organization is on original user management, it must first be migrated to centralized user management. The condition is that the source organization must be a single-site organization.

• This could involve deactivating and deleting any sandboxes associated with the source organization by following the steps in “Deactivate a sandbox”.

• This is a non-disruptive backend process performed by Atlassian Support, with support from our development teams. No changes or downtime will occur at the App or site levels during this process.

Phase 3: Consolidation Pre-Flight Checks

Atlassian will run pre-flight checks to identify blockers. The steps to clear these blockers can vary depending on the type of blocker, for example, having a domain claimed in the source organization.

For a detailed list of common blockers, please refer to Resolving preflight blockers for an organization consolidation.

The comprehensive list will be shared with you, along with the steps to clear the blockers. Expect some back-and-forth with Atlassian Support to resolve any issues.

Phase 4: Dry Run Report

A Dry Run simulates the consolidation without making changes:

• Purpose: Preview expected changes, such as groups whose names will change after the merge.

• Content: Includes technical details (account IDs, group IDs, site IDs). Support will help translate these into understandable terms.

• Approval required: The consolidation can't proceed without your written approval of the Dry Run report.

• Timing: The actual consolidation should occur within 24-48 hours after the Dry Run approval to minimize disruptions.

Phase 5: Consolidation Execution

Once the Dry Run is approved, the development team will execute the consolidation during the scheduled window. The process involves:

1. Userbase merge: Users, groups, and admin settings are combined. This typically takes 2–4 hours.

2. Data-layer merge: (Teamwork Graph) — Cross-product data and relationships are merged. For most organizations, this can be completed within 1 hour. Very large organizations may take longer.

3. Key points:

   • The admin hub will be in read-only mode during the migration (no downtime for products).

   • Site admins and trusted users must become organization admins or be demoted to regular users.

   • After consolidation, all users from both organizations are part of a single unified userbase and are managed via the Directory tab. Users will only have access to sites and products to which they have been explicitly granted access.

   • Groups with the same name across sites will be renamed to avoid conflicts.

   • Individual site transfers will no longer be available after centralized user management is enabled.

The admin hub for both organizations will be in read-only mode during this process.

Section 7: After the Consolidation

Once complete, verify the following:

• ✅ User access — Confirm that users have the correct product access and roles.

• ✅ Group names — Review renamed groups.

• ✅ Licensing — Verify that license counts and plan tiers are correct. Ensure no license breaches occurred.

• ✅ Marketplace apps — Confirm that apps are functioning correctly and subscriptions are properly aligned.

• ✅ Domain verification — Re-verify any domains that were removed during the pre-consolidation phase.

• ✅ SSO / SCIM — Reconfigure user provisioning (SCIM) in the destination organization.

• ✅ Atlassian Guard — Re-enable Atlassian Guard if it was deactivated as part of the consolidation, if required.

Contact Support

If you are planning to consolidate your organizations or have questions, contact our support team and follow these steps:

1. Go to the Atlassian Support portal.

2. Under “What can we help you with?”, choose Technical Issues and Bugs.

3. Under “Which product is this for?”, select Cloud Administration.

4. Fill in the required details, including your site URL (for example, yoursite.atlassian.net) and the consolidation details.

5. If the destination organization is an Enterprise organization, be sure to provide a site URL from the destination organization, not the source organization.

6. Be sure to include the source organization and destination organization details.