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Migrating to Atlassian Cloud: A Complete Guide

Many teams across a variety of industries rely on Atlassian for software development, project management, and boosting their service teams. As we inch closer to the previously-announced deprecation of Atlassian Server — which is set to occur in 2024 — your company might find itself scrambling to understand when, how, and if it should migrate its Atlassian products to the cloud.

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The advantages of moving from an on-premise setup to Atlassian Cloud are certainly appealing. A successful migration can mean a more cost-effective, secure, scalable, and remote-friendly environment. But without proper preparation, migrating to Atlassian Cloud can be a time-consuming, disruptive feat. Already-busy teams, particularly those who haven’t yet executed a migration, may be left wondering where to start, what they’ll need, and how a migration will impact their operations.

Here, we’ll take a deep dive into everything your team should consider before making the leap to Atlassian Cloud. This guide explores how to determine if a migration is right for your team, preparing for and carrying out a successful migration, and making the entire process as seamless as possible.

Why and When to Migrate to Atlassian Cloud

Your migration approach will be unique to your organization's specific requirements and objectives, as there’s no truly universal framework for moving to the cloud. However, there are still several high-level factors every company should consider before embarking on a migration journey to Atlassian Cloud.

Number of Users

One vital migration element to consider is your team’s number of users. A sudden, unexpected increase in users can exceed the critical capabilities of your initial infrastructure — resulting in longer load times, poor application performance, and an overall lack of adoption.

Organizations with more users might need to take a more gradual, hybrid approach to ensure they remain within the bounds of the platform’s limitations. Though the current maximum number for Atlassian Cloud is 10,000 users, companies should understand that reaching that limit, at least right off the bat, can cause significant performance issues. A good rule of thumb here is to consider a hybrid or multi-cloud solution if your team has upwards of 2,000 users.

App Functionality

Depending on your organization’s current Atlassian Data Center or Server plugins and applications — as well as your company’s external tools — you may need to evaluate potential functionality and compatibility. Some legacy Atlassian plugins are not available with Atlassian Cloud, so you’ll need to decide if the resulting reduced functionality is a deal-breaker for your team. Integrations with some tools can also cause issues as you migrate, as Atlassian Cloud customers do not have backend platform access for system-level API calls or scripting. Before you commit to a cloud migration, take the time to identify the value each Atlassian plugin or integration offers your organization, and weigh it carefully against the benefits of implementing a cloud solution.


For organizations in certain industries like healthcare, finance, and manufacturing, adherence to compliance standards, like HIPAA, PCI DSS, and FedRAMP, is non-negotiable. Prior to migrating to Atlassian Cloud, verify whether the solution complies with all applicable regulations. And your team should ensure that both your data flow and operational workflows continue to remain secure and compliant throughout the migration process.

Migration Timeline and Disaster Recovery

Your migration to Atlassian Cloud will require some significant downtime, even in the best case scenario. To keep any disruption to business operations to a minimum, organizations should have a disaster recovery (DR) strategy in place before starting their migration journey. They’ll then be properly prepared if anything goes awry during the migration process.


Ideally, your migration to Atlassian cloud will be a seamless, efficient process. But even if that’s the case, your organization still needs to factor in post-implementation services and support. Many IT teams choose to partner with experts who offer 24/7 support, as these third-party providers can help maintain operational efficiency during data migrations, bug fixes, security patches, and disaster recovery.


Before you determine the best solution for your Atlassian deployment, it’s vital to take stock of the features your organization currently uses and compare them to those available with Cloud and Data Center. The table below shows the top features available in each:


Data Center


Encryption in Transit

Encryption at Rest

Security/Privacy Questionnaire


Password Policy

Uptime SLA (99.9%+)

Security Dashboard


Access Logging


Isolation of Data to Certain Geo


Delegated Administration


Enterprise User Management


Increased User Limits (10K+)


Easy Migration of Add-on Apps


Private Infrastructure


Content Security Monitoring


Key: ✅ = Yes, 🚫 = No, 🟡 = In Progress


One of the most enticing benefits of making the switch to Cloud is the long-term cost savings of a successful deployment. Once the new solution is up and running, your company is likely to see reduced administrative costs associated with fixes, patches, and support. These benefits are balanced by the significant initial investment a migration requires, so organizations should carefully evaluate costs in advance. Consider potential expenses related to data mobilization, additional personnel required, and any necessary third-party support.

Preparing for an Atlassian Cloud Migration

If, after careful consideration, you’ve decided to migrate to Atlassian Cloud, you’ll need to ensure all your ducks are in a row before getting started. Follow these key best practices to prepare for your company’s migration.

Choose Your Migration Method

The best migration method for your organization depends on a variety of factors. Conduct an in-depth assessment of the following elements, among others:

  • Whether your intended destination is an existing Cloud site or a new Cloud site
  • What data you want or need to migrate
  • Which products you plan to move to Cloud
  • Whether you will need to consolidate multiple Cloud or Server instances
  • Estimated downtime, based on your amount of data and number of users
  • Whether your migration will occur in stages or all at once
  • Which add-ons you want or need to migrate

Once you’ve evaluated the factors above, you can more confidently determine which migration approach will best serve your needs. If your organization has a complex migration, limited internal support, specific compliance requirements, a large number of users, or a short timeline, it may be worth teaming up with a third-party solution partner. These providers are specifically trained to help you identify and carry out the migration method that best suits your particular use case.

Determine Your Migration Cadence

Whether your data is completely ready to move to Atlassian Cloud or you’ll need some extra prep time, choosing the right migration cadence is crucial. This choice helps you properly plan for downtime and limit any subsequent disruptions to your operations. The table below outlines four different cadence strategies and when each may be appropriate.

Cadence Strategy

Use if…

Optimize and Shift

  • You want to migrate everything at once

  • You need a shorter timeline and reduced downtime

  • You’re only migrating the data you absolutely need

  • You have adequate time and resources (or a third-party partner) to clean up the server

Lift and Shift

  • You need to migrate to Cloud quickly, with a single downtime window

  • All of your critical apps are available in Cloud

  • You don’t have adequate time or resources pre-migration to clean up the server


  • You want to migrate gradually, in two to four phases

  • You want to clean up and optimize over a longer period of time

  • You cannot migrate in a single downtime window due to data or business complexities

  • Some of your organization’s most critical apps are not yet available in Cloud

Start Fresh

  • You want to work in Cloud immediately

  • You don’t need access to old data or projects in Server

  • You do not want any downtime

Complete All Prep Tasks

Next, you’ll need to ensure your site is totally prepped for your planned migration, using the checklist below:

  • Confirm you’re on a supported Server version. The migration method you select may require you to be on a specific version of your Data Center or Server instance before moving to Cloud.
  • Clean up your Server instance. If you neglect to clean up your Server instance prior to migrating, you could be setting yourself up for poor Cloud performance down the line. Identify which inactive apps, users, workflows, product data, projects, and customizations can be simplified or retired, and eliminate any duplicate data. 
  • Wrap up your pre-migration tasks. To better avoid common pitfalls, Atlassian offers pre-migration checklists for both Jira and Confluence, so review and complete their mandatory and recommended tasks.
  • Develop a runbook. Even the best migration plans aren’t actionable without proper documentation. Craft a detailed runbook to get everyone on the same page, including detailed timelines, step-by-step instructions, and a list of the owners for each migration-related task.

Move Your Apps and Users

By this point, you should have an accurate list of all the apps and users you’ll need in your Cloud instance. Your final list, of course, will be contingent upon which of your critical apps are actually available in Cloud and which users will need access. Once you’ve nailed down these details, it’s time to actually move them over.

Your team can move some apps instantly with automated migration paths, while others require you to first install the Cloud version of the app. For those unavailable on Cloud, you may be able to choose alternative apps that will work on your instance. After installing all of your necessary apps and completing all user preparations, you can migrate your app and user data to Atlassian Cloud.

Communication and Training for an Atlassian Cloud Migration

Your Atlassian Cloud migration will only succeed if your team is well-equipped to handle the transition. To avoid potential migration issues like end-user confusion, adoption resistance, and workflow bottlenecks, communicate the key aspects of the migration to your team members. They’ll then know how it will impact operations and what will be expected of them throughout the process. Offer ongoing training and robust resources for support, and be as open as possible to your team members’ feedback.

An Atlassian Solution Partner can lighten the load of transitioning to Atlassian Cloud and better align the migration with your organization’s overarching business goals. The right partner can help you analyze your processes, build better workflows, and create a roadmap to more seamlessly execute and optimize your deployment. Some also offer end-user, administrator, and program training, along with round-the-clock support, so your IT leaders don’t have to go it alone.

Migrating to Atlassian Cloud

Once you’ve laid down the foundation for your move to Atlassian Cloud, you’re ready to start testing and carrying out the live migration.

Testing the Migration

Running a test migration isn’t optional. It will help you more accurately estimate downtime, validate your data, and identify and resolve potential bugs. Here are the steps involved in running a test migration:

  1. Clean up your data. You likely have existing data in your Server instance that can be simplified, unnecessary, or duplicative. Clean up your data prior to testing to streamline the migration process.
  2. Sign up for your Cloud site. If you don’t already have one, you need to sign up for a Cloud site. Keep in mind, you can run your test to either a trial site or your production site.
  3. Complete your pre-migration checklist. Make sure you’ve ticked off all the items on your pre-migration checklist to ensure your data and team are ready for testing.
  4. Conduct the trial run. Using the instructions in Confluence Cloud Migration Assistant, Jira Cloud Migration Assistant, or Jira Site Import, you can import your necessary data to Cloud. You can then migrate or install any apps you plan to use in Atlassian Cloud.
  5. Review your data and conduct user acceptance testing (UAT). Once you’ve performed your migration, take a good look at your Cloud site to confirm everything went smoothly. Check links to other content and application links to Server products, test your integrations, and make sure any apps you’ve migrated are working properly. You should then have a few end-users conduct UAT by executing some of their common daily functions on the test site. Take detailed notes on any issues you’ll need to resolve. 
  6. Reset your test site. Depending on how your trial went, you may need to delete your data from your Cloud site and begin the process again. 
  7. Tweak your migration runbook. Now that you’ve carried out a trial migration, you can go back to your migration runbook and make any necessary changes. These revisions should help your plan better reflect the actual migration process so it will run as smoothly as possible.
  8. Adjust your change management plan. Now that you’ve gotten a feel for what will change after the migration, you can improve your documentation, training, and communications for the move.

Carrying Out the Migration

You’re finally ready to execute your migration to Atlassian Cloud! Below, we’ll walk you through the steps of a live migration using the Jira Migration Assistant (note that the process is similar for Confluence):

  1. Assess your apps. The Jira Migration Assistant will help you identify which apps you’ve already installed on your local system and which ones you’ll need to assess or prepare for migration. In some cases, you can choose alternative apps for those that are unavailable in Cloud, which eliminates the risk of apps blocking your migration.
  2. Prepare your apps. Next, you’ll connect to your desired Cloud site, install your critical apps, and agree to app migration. The data from each of your apps will be moved from your Server site to its cloud-equivalent version.
  3. Migrate your data. Finally, you can start migrating all of your data. Connect to your cloud site, select your migration options, check for any errors, review your migration, and then run it.

What to Do After an Atlassian Cloud Migration

It’s important to remember that migrating to Atlassian Cloud isn’t a one-and-done effort: it’s a complex, ongoing process that requires quite a bit of follow up. Make your move as effective, efficient, and valuable as possible with these tips:

  • Providing extra support. Any change or disruption to your team’s daily operations can be scary, confusing, and frustrating. Make sure the support you offer extends long after the actual migration so team members are empowered to use Atlassian Cloud to its full potential.
  • Handling ongoing maintenance. Your migration will likely require significant hands-on maintenance to ensure the platform is performing at the highest level possible. You’ll need to keep up with new features, scaling efforts, and technical elements so your team can continue operating efficiently.
  • Optimizing your implementation. You can’t expect your migration to magically fix all of your process roadblocks or collaboration issues. You’ll need to tweak your implementation and optimize your new Cloud instance to better support and improve your unique workflows.

A strong Atlassian Solution Partner can take post-migration burdens off your team’s shoulders. Instead of having to invest in new IT hires or adding to the load of already-overworked staff, the right partner can help you plan, implement, and manage a successful migration. They’ll maximize the efficiency — and ROI — of your Cloud solution by tailoring Atlassian’s tools to fit your team’s needs and maintaining a high-performing, secure environment.

Make Migrating to Atlassian Cloud Fast and Easy

Migrating to Atlassian Cloud will soon be necessary for many organizations as Server’s deprecation date approaches. To reduce downtime, ensure proper preparation, and optimize deployment, companies need an expert Atlassian Solution Partner to take the reins.

Contegix is the only end-to-end Atlassian Platinum Partner that offers everything your organization requires for a successful Cloud migration. With best-in-class professional services, managed application administration, and robust support, Contegix can help your team adopt, migrate, and maximize all of your Atlassian tools. The result is a more productive, secure, and streamlined business operation.

Contact Contegix today to learn more about how its team of experts can help your company navigate the complexities of migrating to Atlassian Cloud.