Atlassian Cloud Migration: Common Challenges and How to Avoid Them

Moving to Atlassian Cloud isn’t just about transferring data from one environment to another. For most organizations, it’s about preserving years of custom workflows, Marketplace apps, integrations, permissions, and business-critical data while keeping daily operations running smoothly.

The challenge isn’t the migration itself. It’s ensuring nothing important breaks along the way. A missed dependency, an incompatible app, or poorly mapped user accounts can lead to unexpected downtime, security gaps, or frustrated teams after go-live. As the end of Atlassian Data Center support approaches, organizations have less flexibility to delay planning and more pressure to execute migrations with confidence.

The good news is that most migration challenges are predictable. With the right preparation, you can identify risks early, reduce disruption, and move to the cloud with minimal impact on your users.

In this guide, we’ll explore the most common Atlassian Cloud migration challenges, why they happen, and the practical steps you can take to avoid them.

Why Planning Early Matters

Waiting until the last minute rarely makes an Atlassian Cloud migration easier. Over time, Jira and Confluence environments become more complex. New Marketplace apps are added, workflows evolve, integrations increase, and more teams begin relying on the platform for their daily work. The longer an environment grows without review, the more effort it takes to migrate successfully.

Starting early gives your team time to assess the current environment, remove outdated configurations, validate app compatibility, and test migrations before moving production workloads. It also reduces the pressure of working against a fixed deadline and allows you to schedule migration around business priorities instead of reacting to them.

Early planning isn’t just about reducing technical risk. It gives administrators, project owners, and end users enough time to prepare for changes, making adoption smoother after the migration is complete.

If you’re beginning your migration journey, our guide on Atlassian Data Center to Cloud Migration explains the migration timeline, key milestones, and how to build a phased migration strategy.

Why Atlassian Cloud Migration Is More Than Moving Data

Atlassian Cloud migration isn’t a lift-and-shift exercise. It involves moving an entire ecosystem of projects, workflows, permissions, users, apps, and integrations while ensuring teams can continue working without disruption.

Most Jira and Confluence environments evolve over several years. As organizations grow, they introduce custom workflows, automation rules, Marketplace apps, integrations with third-party platforms, and governance policies that support day-to-day operations. These configurations often become deeply embedded in business processes, making migration far more complex than simply transferring issues and pages.

A successful migration starts with understanding what exists in your environment and determining what should move to the cloud. Every workflow, integration, and permission model should be reviewed to ensure it remains relevant, compatible, and aligned with your organization’s current needs. This approach reduces unnecessary complexity, improves long-term maintainability, and helps teams take full advantage of cloud capabilities.

Planning at this stage also helps identify potential risks before migration begins. Unsupported Marketplace apps, outdated customizations, and complex permission structures are much easier to address during planning than after production workloads have moved.

With a clear understanding of your environment, you can build a migration strategy that minimizes disruption and sets your teams up for long-term success in Atlassian Cloud.

Common Challenges During Atlassian Cloud Migration

Most migration issues are predictable. They usually stem from legacy configurations, unsupported customizations, or inadequate planning rather than the migration itself. Understanding these challenges early helps you reduce risk, avoid costly surprises, and keep your migration on schedule.

1. Marketplace Apps and Integrations

Marketplace apps are one of the biggest roadblocks during Atlassian Cloud migration. While many popular apps have cloud versions, they don’t always offer the same features or behave exactly as they do in Data Center. Some apps require configuration changes, while others have no cloud equivalent.

Integrations also need careful attention. Connections with tools like Slack, GitHub, Jenkins, Microsoft Entra ID, monitoring platforms, or internal applications often require new authentication methods, updated APIs, or configuration changes after migration.

Reviewing app compatibility and validating integrations before migration helps prevent unexpected disruptions after go-live.

2. Data quality and user mapping

Migrating data is only valuable if it remains accurate and usable after the move. Missing attachments, broken links, incomplete issue history, or incorrectly mapped users can affect reporting, collaboration, and auditability.

User mapping is particularly important. If user accounts or email addresses don’t align between your Data Center and Cloud environments, issues, comments, and notifications may be assigned incorrectly, creating confusion for teams after migration.

Running test migrations and validating sample projects helps identify these issues before production workloads are affected.

3. Permissions, roles and access

Permissions and roles in cloud follow a more global model than many legacy server setups. It is common to see complex project‑level permission schemes and local admin roles in Data Center that do not map directly to cloud.

If you migrate without reviewing permissions, you may accidentally grant too much access to sensitive projects or block users from work they need. You also miss a chance to simplify roles and align them with current governance and compliance requirements.

At the same time, Atlassian is introducing new ways to bundle tools and capabilities for different types of teams. Atlassian Collections group products, AI capabilities, and platform features for software, service, and business teams. Understanding these collections helps you design a cloud setup that is easy to manage and intuitive for users.

4. Downtime and business disruption

Jira and Confluence are part of daily work for most teams. If Atlassian cloud migration happens at the wrong time, such as during a sprint, a release, a major incident, or a busy quarter‑end period, you can slow down projects and affect customers.

Without a clear backup and rollback plan, your options are limited if something fails halfway through the migration. Teams might be locked out of tools or stuck with partial data until problems are resolved.

Careful scheduling, clear success criteria, and realistic rollback steps are essential. Migration should feel like a planned maintenance window, not an emergency.

5. Change management and new features

Technical success does not automatically mean user success. Cloud has a different interface and adds new features, including AI‑driven capabilities that work across tools. If you move without explaining what is changing, why the move matters and how users benefit, you risk confusion and resistance.

Our Atlassian Teamwork Graph guide explains how Atlassian connects work items, people, pages and other data into a unified graph. This graph powers smarter search, recommendations and insights. On top of this, Atlassian Rovo introduces AI‑based search, chat and specialized agents that help teams find answers faster and take action on information.

Explaining these concepts in simple terms helps users see cloud as an upgrade, not just a forced move. Short walkthroughs, Q&A sessions, and clear “before and after” examples make adoption smoother.

How To Avoid These Atlassian Cloud Migration Challenges

The good news is that these challenges are predictable, and you can avoid most of them with a structured approach. Here are practical ways to reduce risk and keep Atlassian cloud migration under control.

Run a full audit before you touch production

Start by listing all projects, spaces, users, apps, integrations, and customizations in your current environment. Identify what is critical, what is used occasionally, and what can be retired. This helps you avoid moving old complexity into the cloud.

Use Atlassian’s migration tools and checklists

Take advantage of Atlassian’s Cloud Migration Assistants for Jira and Confluence, along with official pre‑migration checklists. These tools help you find unsupported data, app compatibility issues, and user mapping problems early. Running these checks ahead of time prevents surprises during cutover.

Clean and simplify your configuration before migration

Archive or remove inactive projects and spaces, simplify workflows, and reduce duplicate or unused custom fields. A cleaner configuration is easier to test and migrate and reduces the risk of performance issues in the cloud.

Test app behavior and integrations in a sandbox

Do not rely on theory alone. Set up a non‑production cloud site and run test migrations for a subset of data. Validate that apps behave as expected and that integrations work end to end. Fixing issues in a sandbox is much easier than fixing them in production.

Plan the order of operations carefully

The order in which you migrate users, projects, and data can significantly affect the outcome. Align user accounts and email addresses before migrating projects to ensure issues, comments, permissions, and notifications are assigned correctly. Taking this step early helps prevent data mapping errors and preserves ownership and historical records.

Define clear cutover, backup, and rollback steps

Write down your migration runbook with exact tasks, owners, timing, and success criteria. Take full backups before cutover and decide in advance when you will roll back versus continue if problems appear. This gives your team confidence and reduces stress.

Invest in communication and short training sessions

Tell users what will change, when it will happen, and why it matters. Provide simple guides and short training sessions focused on the new cloud interface, key differences, and the benefits of features powered by Teamwork Graph and Rovo. Clear communication reduces resistance and speeds up adoption.

This structured approach helps reduce migration risks by validating data, reviewing permissions, testing integrations, and verifying system readiness before production cutover.

A Practical Framework For Atlassian Cloud Migration

To make Atlassian cloud migration easier to manage, we recommend breaking it into six clear phases. This keeps both technical teams and business stakeholders aligned.

Understand your current environment

Begin with an inventory. List Jira projects, Confluence spaces, user groups, workflows, custom fields, apps and integrations. Mark what is business‑critical, what is useful and what is unused or outdated. This gives you a clear picture of what you are really migrating.

Decide your cloud strategy and scope

Choose the right cloud plan based on your organization’s size, performance needs, compliance requirements, and data residency requirements. Decide whether to migrate all instances and teams at once or in phases. Many organizations start with less critical areas to learn and refine their approach before touching core systems.

Clean and prepare data and permissions

Use migration as a chance to tidy up. Archive old projects and spaces that are no longer needed. Simplify overly complex workflows and remove duplicate or unused custom fields. Standardize user accounts and email formats. Review permissions and map them to a simpler, more secure model that works in the cloud and supports audit and compliance needs.

Review apps, integrations and automations

Compare your current Marketplace apps with their cloud versions. Decide which apps you will keep, replace, or retire. For integrations, document how each connection works today and how it should work in cloud. Build and test updated integrations in a non‑production environment. This step is also a good time to remove old scripts or custom code that adds risk but no longer delivers value.

Plan cutover and rollback with clear criteria

Choose migration windows carefully, avoiding key sprints, product launches, or seasonal peaks. Take full backups of your environment before migration. Define what “success” looks like for cutover. For example:

• All selected projects and spaces are present in the cloud
• Key apps and integrations work as expected
• Users can log in and see the right work and permissions

Document simple, practical rollback steps in case you need to pause or revert. Even if you never use this plan, having it reduces stress for everyone involved.

Support users during and after migration

Treat Atlassian cloud migration as a change for your teams, not just your tools. Share clear timelines, screenshots of the new interface, and short descriptions of what will feel different. Run quick training sessions or office hours for Jira admins, project leads and regular users. After go‑live, collect feedback and fix small issues quickly. This builds trust and helps people settle into the new environment.

Final Thoughts On Atlassian Cloud Migration

The 2029 deadline may feel far away today, but larger and regulated organizations often need many months, and sometimes years, to move safely. Starting Atlassian cloud migration early lets you work at a comfortable pace. You can test, adjust, and communicate clearly instead of rushing when time is short.

A well-planned migration gives your teams a modern Atlassian environment that is faster, more secure and more intelligent. Cloud brings automatic updates, stronger security controls and new AI features built on the Teamwork Graph and Rovo. In everyday terms, you move from tools you must maintain yourself to tools that keep improving and helping your teams work better.