Best practices for merging cloud Jira instances

Written by
Gal Fatal
Atlassian expert & Community leader
June 27, 2023
min read

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In today's fast-paced business environment, organizations often manage multiple Jira instances for a variety of reasons, such as mergers, acquisitions, or independent team deployments. However, maintaining separate Jira instances can lead to inefficiency, data fragmentation, communication challenges, and high costs.

Merging Jira instances into a single instance can be a complex process that requires careful planning and execution. However, consolidating Jira instances can significantly benefit Jira administrators, users, and stakeholders. This article will explore when and why to consider merging Jira instances, as well as the best practices for executing the merge.

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When and why to consider merging Jira instances?

Organization consolidation

If different teams, departments, or organizations within a company are using separate Jira instances, merging them into a single Jira instance can promote better collaboration, streamline processes, and enhance visibility across the organization. It allows for a centralized and unified view of projects, issues, and resources, enabling better decision making and more efficient project management.

Merger or Acquisitions

When organizations merge or acquire one another, they typically combine different systems, processes, and technologies. This includes their separate Jira instances, the backbone of project management and issue tracking within their operations. Multiple Jira instances can create fragmentation, inefficiency, and gaps in team communication. Therefore, merging these instances becomes necessary to adjust processes, consolidate data, and promote collaboration among the merged entities.

Standardizations and process alignment

Aligning processes across projects and teams is another significant advantage of merging Jira instances. When multiple Jira instances exist, each with its own customizations, workflows, and configurations, it can create fragmentation and limit collaboration. Organizations can establish standard practices and align processes across projects and teams by consolidating these instances into a single, unified Jira instance. Merging the instances allows organizations to define and enforce standardized workflows, issue types, and field configurations. This consistency promotes clarity, reduces confusion, and enables easier adoption for new team members.

Cost optimization

Managing multiple instances involves distributing administrative tasks across different instances, such as user management, permission settings, and plugin updates. This can be time-consuming and resource-intensive, requiring separate efforts for each instance. By merging the instances, organizations can centralize administrative tasks, simplifying the management and reducing the overall administrative workload. This consolidation enables better resource allocation, allowing administrators to focus on value-added activities rather than spending excessive time on repetitive tasks.

Licensing costs also can be influenced when merging instances. The more users you have on one instance, the less you pay per user. For example, if you have two sites—one with 650 users and the other with 850 users, both in the premium plan—you’re currently paying $74,000 for the first instance and $89,500 for the second instance. Together, that’s $163,500 per year. If you move to one instance with 1500 users, you will instead pay $134,500—a significant annual savings.

Use Atlassian’s “Compare plans and pricing” page to check how much you can save. If you have paid apps, similar savings can be applied to each app. You should check the pricing for each app and calculate how much you may save after the instances merge.

Improve reporting and analytics

Multiple Jira instances often mean that project data is spread across different systems, making it challenging to generate unified reports or perform in-depth analyses. By merging the Jira instances, organizations centralize their project data into a single repository, allowing project managers and other stakeholders to view all their data more easily. 

Jira provides options for generating reports using templates, gadgets reports, and JQL that can consolidate data from multiple projects in one Jira instance. In addition, many apps in the Atlassian marketplace, such as eazyBI Reports and Charts for Jira or Custom Charts for Jira Reports and Jira Dashboard Filter can add reporting capabilities. However, since these apps all act as a reporting solution for one Jira instance at a time, merging Jira instances into one instance leads to unified reporting capabilities.

Improve user experience

When organizations maintain multiple Jira instances, users often have to switch between different instances to access the projects and information they need, which can also require a different username and password. This can be time-consuming, particularly for team members who work across multiple projects or teams. By merging the instances, users can access all projects and information from a single login, eliminating the need to switch between multiple systems. This simplification of user access makes navigating and interacting with the Jira environment easier and more efficient, leading to increased productivity and a better overall user experience.

Best practices for merging

Plan the merge scope

Before starting with the technical aspects of the merge, it's essential to define the merge scope. This can be an excellent opportunity to check your instances, deciding which projects, configurations, or issues should be merged and included in the new merged instance. Cleaning the instances of unnecessary configurations and old issues is recommended before merging. The more configurations you have on your instances, the more complex the merge will be. Review configurations like workflows, automation rules, and custom fields, and clean up what you can. To explore your configurations, you can use a tool like Salto, which allows you to see the dependencies of each element, helping you to understand where the element is in use and which other elements depend on it. This is critical when deciding whether or not to delete something. See also Best Practices for reducing Jira customizations for more insights into how to clean up your configurations and old issues.

Choose migration tools/method

Merging between instances can be a complex process. It’s highly recommended to utilize process-supporting tools in order to overcome challenges and merge successfully. Let's explore some options for tools and methods.

  1. Atlassian provides a new cloud-to-cloud-migration feature that lets you migrate and merge one or more projects, along with their issues, attachments, users, groups, and configurations, from one cloud site to another. To access this feature, log in as an administrator, and from the source instance, select “settings” at the top right corner of the screen. Then select “system” and Migrate cloud site.



Notes for using Atlassian’s cloud-to-cloud-migration feature:

  • This feature is gradually rolling out and may not be visible on your cloud site.
  • This feature is in Beta.
  • Team-managed projects aren’t supported.
  • Please read the following limitations carefully before you decide to use the feature, as it does not cover the migration of all configuration elements. For example, some custom fields, global permissions, and dashboards are unsupported and will not be migrated during the instance merge. See the “What isn’t migrated” table on the “What migrates in a cloud-to-cloud migration” page for more information.

  1. If the Atlassian cloud-to-cloud-migration feature does not fit your needs, you can try to  perform the migration using Jira Data Center in one of two ways.

The first option is to use the Jira cloud migration assistant via Jira Data Center. You will need to back up and import one of your cloud instances to a Jira Data Center you install in advance and then import the result to the target cloud instance using the Jira cloud migration assistant.

The second option using Jira Data Center is to merge the sites in Jira Data Center and import into Jira cloud manually. With this option, you’ll need to create backups of all your Jira Cloud sites, merge the backups in Jira Data Center, and then import the backups into your destination cloud site. Here’s a diagram of this process:


Both options require you to set up a Jira Data Center instance (which can be done with a free trial license) and have a number of limitations. Atlassian specifies that these methods may not work for all customers and recommends that you test them before performing a production migration. Read the instructions and limitations for each option for more information.

  1. If you have small instances without many configurations, consider using a CSV file to export issues from the source instance and import them to the target instance. Import/export will bring only the issues’ data without the history. With this option, you need to handle all configuration differences between the instances manually before you can import the issues, including creating new projects in the target instance. One of the advantages is that this does not require downtime for the source/target instances. Read the section on how to use a CSV file to import issues for more information about the instructions and limitations of this option.
  1. Another option is to use a tool like Salto to merge configurations between instances. Salto can display the configuration differences between instances and merge them for you. You can merge all the differences or pick only what you want to merge. If you use ScriptRunner, Salto also supports merging those scripts, which is a big advantage as merging the scripts manually can be challenging.

If you use this tool, you should complete the instance merge by adding the desired issues from the source to the target instance. The recommended way is to use a CSV file, as described previously.

There are other tools on the market that can assist with the instance merge as well. For example, AtlasMerge is another option that can merge multiple instances together. However, it’s important to keep in mind that it has limited cloud merge support.

Configuration and customization alignment

Merging configurations and customizations is the main challenge when merging Jira instances. It’s recommended to review the instances in advance and look for elements you can unify before the merge. For example, if you have custom fields in both instances that have similar names and usage, consider changing one and then using one version in the target instance. Explore your configurations in both instances. Look for similar workflows, roles, automation rules, and other elements that could potentially be merged into one element. You can use Salto to explore your instances and look for differences and dependencies.

Integration and app alignment

If you use apps from the Atlassian marketplace in the source instance, remember that the tools for merging instances do not move apps or app data and configuration. This step must be done manually. You must install each app on the target instance in advance and resolve the data and configuration merge separately. Some vendors offer instructions for this scenario (for example, see these instructions for the popular easyBI app) but keep in mind that not all vendors give a clear solution. You’ll need to get in touch with each app vendor separately to discuss your options.

Testing and migration

If you have a premium or enterprise support plan, you can create a sandbox for testing environments. This is the recommended way to test your instance merge. Doing so allows you to retry and fix any issues that occurred during the migration or after without disturbing the production source and target instances. See sandbox best practices for more information on how to work with the sandbox. 

It’s recommended to do a user acceptance test and select a group of users, so they can work on and test the migrated projects. These users should use the same account they had in the source instance. Ask them to check the following items:

  • Can you view and edit issues?
  • Can you launch transitions?
  • Can you access reports, filters, dashboards, or agile boards?
  • Can you access the same information you were using in the source instance?

Depending on your chosen method, the merge may require downtime of the target instance. It’s recommended to start the merge action in the evening or on the weekend and allow extra time for fixing issues. Create a banner in advance, and let the users know about the merge and the timing.

Post-merge support and maintenance

After the merge, you’ll want to notify the users and consider canceling the subscription for the source instance to save on costs.

Notifying users:

If you used the cloud-to-cloud migration feature, all users will be migrated to the new instance but won’t get an email notification. So, once you complete the migration and are ready, you should notify all users, providing the link to the new instance. You can also invite them using the Resend invite. See the invite a user page from Atlassian’s documentation for more information.

Canceling subscriptions for the old instance:

Depending on your license plan and budget considerations, you might want to consider canceling the subscription for the old instance. You can cancel your site subscription by going to Administration > Billing > Manage subscriptions and selecting Cancel subscription. It’s recommended to keep the old instance alive for a few months as a backup. In this case, you should remove all user edit permissions so that no one accesses the instance by mistake, as well as post a banner explaining the migration and providing the link to the new instance.

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Merging Jira instances is a complex process that requires careful planning, coordination, and technical expertise to ensure a successful integration. Merging Jira instances involves consolidating separate Jira environments into a unified instance to align workflows, consolidate data, and promote seamless communication and collaboration. This process is essential when organizations merge or acquire one another, ensuring a smooth transition and integration of operations. 

By merging Jira instances, organizations can achieve several benefits, including standardized workflows, consolidated data for comprehensive reporting and analytics, enhanced communication and collaboration, improved resource utilization, and cost savings. The consolidation simplifies user access and authentication, promotes knowledge sharing, and provides cross-team visibility. Merging Jira Cloud instances is a strategic step toward optimizing project management and driving successful outcomes within the merged entities.

Written by
Gal Fatal

Gal Fatal has over ten years of experience in DevOps, ALM solutions, and Agile development using Atlassian solutions. Gal is a recognized expert in Atlassian tools, holding five different Atlassian certifications. He is leading the Atlassian community in Israel, where he has made significant contributions to the development and growth of the community in Israel over the past five years.

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