10 Common Mistakes Teams Make When Moving to Atlassian Cloud

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Migrating to Atlassian Cloud is more than a technical project, it’s a strategic shift. Done well, it unlocks faster innovation, reduced admin overhead, and tighter integration with modern tools. Done poorly, it creates headaches for admins and confusion for users.

Based on lessons learned from real migrations and Atlassian’s own Cloud Migration Center, today I gathered 10 of the most common migration mistakes teams make - with suggestions how you can avoid them.

Planning & Assessment

The first missteps usually happen before the migration even begins.

1. Skipping the App Audit

Marketplace apps are the backbone of many Jira and Confluence instances, but not all have a Cloud version. Even when they do, functionality can differ. Teams that migrate without reviewing their apps risk discovering critical gaps after go-live.

Tip: Run an app assessment early and confirm which apps have Cloud equivalents, replacements, or integration alternatives.

2. Underestimating User & Identity Management

Cloud identity management is different from Server and Data Center. Atlassian accounts, centralized domains, and Atlassian Access all play a role. If these aren’t aligned before migration, you can run into login issues or account duplication later.

Tip: Clean up inactive users, verify your domains, and decide whether you need SSO before making the move.

Data Quality & Structure

Once you know what you’re moving, the next question is how much of it you actually need.

3. Ignoring Data Clean-Up

Many organizations treat migration as a pure transfer - but carrying years of outdated projects, custom fields, and unused workflows only makes the new Cloud environment harder to manage.

Tip: Take the opportunity to archive or remove what no longer adds value. Migration is the perfect moment for a fresh start.

4. Migrating Without a Test Run

Even with the best planning, surprises happen. Teams that skip a trial migration often only discover broken workflows, missing data, or permission mismatches once they’re live in Cloud.

Tip: Always do a test run. A sandbox migration helps validate data, permissions, and integrations in a safe environment.

Customization & Functionality

Server and Data Center offer a wide degree of customization, but not everything translates directly to Cloud.

5. Assuming Feature Parity With Server

Custom scripts, workflow conditions, or database-level tweaks may have no direct equivalent in Cloud. Migrating without understanding these differences can break critical processes.

Tip: Identify customizations early and redesign them using Cloud-native automation or Marketplace alternatives.

6. Overcomplicating Permissions

Complex permission schemes often create problems during and after migration. Users may lose access or, worse, gain access they shouldn’t have.

Tip: Simplify permissions before you migrate. Clearer, leaner schemes make for a smoother transition and easier governance in the long run.

Governance & User Adoption

Migration is as much about people as it is about technology.

7. Treating Migration as a One-Time Lift-and-Shift

Simply moving everything over without review might be faster, but it’s also a missed opportunity. Cloud migration is the right time to streamline workflows, reduce custom fields, and improve consistency across teams.

Tip: Approach migration as a modernization effort, not just a relocation.

8. Underestimating Change Management

End users are the ones who feel the change most directly. If they aren’t informed or trained, resistance is inevitable. A new interface or restructured workflow can cause confusion if rolled out without context.

Tip: Communicate early, highlight the benefits of Cloud, and provide training sessions or documentation to support the transition.

Risk & Performance

Even the best-prepared teams need to think about what happens if things don’t go to plan.

9. Skipping the Rollback Plan

Migrations can fail. Without a fallback plan, downtime can stretch into days.

Tip: Keep a Server or Data Center backup and document the steps for rollback. Even if you never need it, knowing it exists provides peace of mind.

10. Overlooking Cloud Limits

Cloud offers scale, but it also has limits - automation rule caps, API rate limits, storage quotas. Teams that assume Cloud will behave exactly like Server often run into performance issues or blocked automations.

Tip: Review Atlassian’s Cloud limits and factor them into your planning. It’s better to design around them than to be caught off guard.

Common Mistake	How to Avoid It
Skipping the App Audit	Run an app assessment early and confirm Cloud equivalents or alternatives.
Underestimating User & Identity Management	Clean up inactive users, verify domains, and decide if SSO is needed.
Ignoring Data Clean-Up	Archive or delete outdated projects, workflows, and fields before migration.
Migrating Without a Test Run	Perform a sandbox migration to validate data, permissions, and integrations.
Assuming Feature Parity With Server	Identify critical customizations and redesign with Cloud-native options.
Overcomplicating Permissions	Simplify schemes for smoother migration and easier governance.
Treating Migration as a One-Time Lift-and-Shift	Use migration as a chance to streamline workflows and modernize processes.
Underestimating Change Management	Communicate early, provide training, and explain Cloud benefits to users.
Skipping the Rollback Plan	Keep a backup and document rollback steps in case migration fails.
Overlooking Cloud Limits	Review automation, API, and storage limits in advance and design around them.

Migrating Connected Tools and Historical Data

When planning a Cloud move, it’s important to look beyond Jira itself. Many teams also need to migrate or sync data from connected tools such as Azure DevOps, ServiceNow, GitHub, Trello, or Notion. This is where solutions like Getint, available on the Atlassian Marketplace, can help.

With Getint you can choose the right approach for your needs:

• One-time data migration – move historical records safely into Jira Cloud, keeping full context for compliance, reporting, or knowledge transfer.

• Continuous integration (or sync) – keep Jira Cloud aligned with other platforms on an ongoing basis, so collaboration continues seamlessly across teams working in different systems.

Both approaches can be valuable depending on whether your priority is consolidation into Jira Cloud or maintaining long-term cross-tool collaboration.

Including migrations and integrations in your planning ensures you don’t create silos or lose context during the move.

Wrapping Up

Atlassian Cloud delivers huge benefits - but migration is rarely a “flip the switch” event. Success depends on preparation: auditing apps, cleaning up data, simplifying permissions, and guiding users through the change.

Think of migration not as the end of a project, but as the start of a new way of working.

Done right, it’s a chance to modernize processes, embrace automation, and give teams a better platform for the future.

Have you already completed a Cloud migration? What challenges did you face, and what do you wish you had known earlier? Share your experiences below to help others on their journey.