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Practical Recommendations for Cleaning and Organizing Your Atlassian Instance



Many organizations begin using Atlassian tools organically—a team adopts them, finds they streamline work and/or improve efficiency, and over time, they gain broader traction throughout the organization. Multiple teams may spin up different instances or use the tools in different ways. In time, the tools become business-critical, but due to the way in which they were adopted, obsolete projects accumulate and seemingly small differences in workflows and custom fields increase. Eventually, even though the tools were designed to help teams collaborate, the abundance of seemingly small differences means day-to-day work is negatively impacted.

Even organizations that start using Atlassian tools more purposefully often find that clutter develops over time, which makes it challenging to make changes to these tools. For example, companies may need to shift to a cloud deployment option, instances might need to be migrated, and tools must be scaled to accommodate corporate growth. Because of their impact on granular data, like custom fields and workflows, initiatives like these are significantly more complex if that data has grown to unwieldy proportions, especially if the organization has not yet established formal governance processes.

In this whitepaper, we explore the challenges organizations face when their Atlassian instances become messy or unwieldy and offer practical guidance for cleaning up Jira Service Management, Jira, and Confluence. In addition, we provide a comprehensive list of best practices for maintaining an optimal Atlassian environment once cleanup has been undertaken.


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Before and After Cleanup: Challenges of a Messy Instance and Benefits of a Clean One

Without regular, focused maintenance, organizations often find that their Atlassian tools become cluttered: new, sometimes duplicate projects get added; new workflows are created, some with only slight differences from existing ones; there are too many custom fields to count; and everyone is using different nomenclature— often for the same thing. JQL queries are slow and return results that aren’t relevant. Eventually, the system can become so cumbersome to work in that users cannot find the information they need to complete work efficiently, and they start running processes outside it. Some organizations may even experience performance issues and make hardware investments to resolve them, only to find that doesn’t solve the underlying problem.

Following are several other key challenges that organizations face when their Atlassian instances become unwieldy, and the benefits realized once an instance has been purposefully streamlined.


Additional Challenges of an Unwieldy Instance


  • System Performance Issues
    A messy instance can cause issues beyond day-to-day usability—it can negatively impact performance by slowing the system down and making it unstable. Many organizations instinctively look to better, more powerful hardware to solve the issue, and while this may have a positive impact in the short run, it doesn’t address the root problem. The overabundance of unnecessary projects, duplicate workflows, etc., that are causing the problem will inevitably continue to grow, and the problem will reoccur. After a cleanup, many organizations benefit from overall performance improvements like increased speed and stability, without having to invest in additional hardware.

  • Lack of Visibility and Difficulty Reporting
    A messy instance is a good indicator that teams across the organization are working in different ways. If every team is using different methodologies, different nomenclature, and different fields, it limits visibility into work being done. This makes it more difficult for teams to collaborate, whether that’s around developing new features and enhancements or responding to critical incidents and disruptions to service. Further, it makes it nearly impossible to pull comprehensive, cross-functional reporting that would indicate bottlenecks and help teams work more efficiently. A clean instance increases visibility so that teams can collaborate effectively, and leadership can pull essential, organization-wide reporting.

  • Inability to Scale or Migrate
    A messy Atlassian instance significantly increases the complexity of scaling to meet evolving business needs. It even makes it difficult for individual contributors to move to another team internally or work cross-functionally: the new team may use different workflows and nomenclature. From an administrator perspective, it limits the ability to adapt the system to business needs. Without a cohesive structure, a simple change like the addition of a new field may need to be made manually to dozens, if not hundreds, of different projects. Similar issues are only magnified when trying to scale the system to accommodate new teams, or teams of teams, acquired through mergers and acquisitions.

Similarly, a cluttered Atlassian instance makes it very challenging to merge instances or migrate to Atlassian Cloud. The more complex the system, and the more projects, issues, workflows, and data there are, the more complex, time-consuming, and risk-prone a merge or migration will be. Cleaning house — consolidating, archiving, or deleting unused workflows and projects, and even Confluence pages and attachments, will significantly simplify the migration process.


Benefits of a Clean Atlassian Instance

In stark contrast to the experiences described above, once an instance has been cleaned up, many organizations find that streamlined processes drive efficiency and enable teams to work more quickly, more accurately, and more collaboratively. Users are more apt to adopt the tools and prefer to work within them, further increasing efficiency and collaboration. At an organizational level, streamlined reporting means leadership can map work to business strategy, make better, more informed business decisions, and more readily identify and address bottlenecks. As a result, the organization sees a better return on their investment in Atlassian tools.

Organizations may realize financial benefits above and beyond the increased efficiency of their workforce too: better tool performance means fewer outages and/or issues and fewer ticket submissions to IT, and even reduced administrative overhead. Further, it becomes much more straightforward to scale the tools as they grow, whether that growth is organic or through mergers and acquisitions. And for organizations with a cloud-first approach, migration to Atlassian Cloud becomes a much more achievable goal.


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Practical Recommendations for Cleaning Up Jira Service Management

In considering Atlassian cleanup, it’s not uncommon to think first of Jira, and then of Confluence. These are both business-critical applications, and it makes good sense to direct much of your time and effort toward them. However, at Isos Technology, we often recommend taking a business service approach to cleanup, and this means looking first at Jira Service Management (JSM). In today’s business and IT environment, all organizations are service organizations, and JSM often sits at the center of an organization’s Atlassian applications. If an unwieldy Atlassian instance is causing problems, they will often be reflected as tickets in JSM.

In the following paragraphs, we provide a high-level roadmap for cleaning up your JSM instance and streamlining service delivery.

  • Clean Up Request Forms
    The first step in cleaning up your JSM instance is to look at how the ITSM team is providing services to other IT teams, as well as business teams. At a high level, you’ll want to look at not just what types of requests are coming in, but how people are making the requests—the language they are using—so that you can make sure the language you use for request types makes sense to the requestors. You will also need to identify what information is needed to fulfill those requests. Then, you can use form builders to develop detailed intake request forms that ensure all relevant information is being captured upfront. 
  •  Analyze Tickets and Issues and Establish Metrics
    Next, you’ll need to analyze what types of tickets or issues are coming in to determine what services they relate to, and what teams will need to be involved in addressing them. You will also want to look at which issue types are just things that happen now and then, things that are consistent and ongoing (like provisioning and de-provisioning new employees), or if they are indicative of systemic problems that need long-term and perhaps labor-intensive solutions.



Following are some things to consider when analyzing tickets and issue types:

  • What types of tickets are coming in? Grouping tickets by issue will help you identify where your customers are encountering roadblocks. That way, you can direct effort to get systems in place that minimize these issues, and/or streamline the way these issues are resolved so that you free up bandwidth.
  • How long do certain ticket or issue types take to resolve? Comparing this against volume will help you understand bandwidth and support better resource planning.
  • What teams or departments are neediest and/or the least needy? Perhaps those squeaky wheels have underlying issues that need to be addressed with larger, more long-term projects. Conversely, just because certain groups aren’t making requests, doesn’t mean they don’t need help. They may be suffering in silence. Either way, you’ll want to prioritize work by greatest need and business impact while balancing focus across departments.

Once you've analyzed the tickets and issues that are coming in, you can create reports for measuring key metrics on an ongoing basis which will help you identify issues sooner and make future cleanups easier. You can also create playbooks outside of JSM, like in Confluence, that document common types of issues and the processes for resolving them. This will help identify places where you can align teams to similar ways of doing things, and make it easier to spin up new workflows for similar types of issues. 

  • Clean Up Your Workflows
    Once you’ve analyzed the data, you can see what types of tickets will follow a given workflow and make sure the workflows capture all of the relevant steps. Each team should have autonomy over what their workflows look like— JSM is flexible enough to meet the unique needs of each team. Still, you should aim for these to be as simple as possible, and for there to be as few workflows as necessary, while ensuring that nothing has to take place outside the system. Another thing to keep in mind is how and when the requester needs to be updated about progress on their ticket. They don’t need to see everything behind the scenes, but they do need to be reassured that progress is being made.

    Once the ITSM team’s processes for request intake are dialed in, you can extend this effort to other business teams like facilities, human resources, legal, and marketing, to help them clean up and streamline their own intake processes. A best practice is to create a single location where customers across the company can go to submit requests of all types, regardless of which team might be fulfilling them, so they don’t have to remember how to get to different portals.
  • Clean Up Your Knowledge Base
    If you are using Confluence to power a knowledge base or wiki so that customers who come to your JSM portal can self-serve, rather than submit a ticket, yet you are still seeing tickets come in for issues that could be resolved on a self-serve basis, you may need to prioritize cleaning up your knowledge base. If your Confluence knowledge base has too many pages, duplicate pages, or pages that are not structured well, it may be returning results that are not helpful to your customers, which will only serve to add to their frustrations. Consider it an opportunity to better structure your existing self-help content, and to come up with a list of useful content that needs to be created based on common issue types.

For more information on cleaning up Confluence, see Section 4.

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Practical Recommendations for Cleaning Up Jira

Jira is one place where duplicate or obsolete projects and workflows and other clutter tend to accumulate, and where you are likely to see a significant impact in performance because of it, particularly if you do not have a governance board in place, and/or you do not have processes in place for regular system cleanup and maintenance. A messy Jira instance can impact efficiency, impede collaboration, and make cross-functional reporting very challenging. Once cleaned up, however, work is streamlined, teams gain the visibility necessary to collaborate, and better reporting makes it easier to identify and resolve roadblocks and issues.




In the following paragraphs, we provide a high-level roadmap for cleaning up your Jira instance.

  • Clean Up Users and User Groups
    Cleaning up users and user groups is one of the more straightforward tasks in Jira cleanup, although depending on your organization’s systems and processes, it may require some manual outreach. It consists of identifying and deleting inactive users, consolidating user groups, where possible, and confirming their permission schemes.
    • Delete Inactive Users
      It’s a best practice to delete users when they leave the company, both for security reasons and to free up user licenses, but it doesn’t always happen as it should. Pull a list of users by the last login date. Confirm that users who have not logged in recently are no longer employed with the company, or have moved to roles where they no longer need seats before removing them.
    • Consolidate User Groups and Confirm Permission Schemes
      Audit your user groups and permission schemes. Identify any user groups that overlap and see if these can be consolidated. Then, confirm whether each group needs global permissions or project permissions, and refine access accordingly.
  • Delete or Archive Old Projects and Issues
    Any Jira instance that has been in use for several years will accumulate projects and issues that are no longer active. Perhaps the work on them has been completed, or the organization decided not to pursue them. Whatever the reason, these inactive projects and issues clutter the system, cause it to return inaccurate results, and slow it down. Depending on your organization’s policies and whether you need to maintain history for audit purposes, inactive projects and issues can both be deleted or archived. More recent versions of Jira allow for easy archiving and restoring of projects and issues, and although this minimizes clutter, you may not see the performance gains you would if you deleted them altogether.

Recommended Reading

Looking to learn more about how to archive projects and issues? Here are two great resources.

          Atlassian Support: Archiving a Project
          Atlassian Support: Archiving an Issue

  • Clean Up Workflows
    Over time, it’s common for the number of workflows within an instance to grow significantly, and this is especially true in organizations that lack a formal governance board or have decentralized tool administration. It’s also common for teams that do similar types of work to have duplicate workflows or workflows with slight variations, and these can be consolidated.
    • Delete Inactive Workflows
      The fewer workflows there are, the easier the system is to maintain and support, so deleting inactive workflows and workflow schemes is a straightforward first step in overall workflow cleanup. First use an app like Admin Toolbox for Jira to identify inactive workflows, then use the scripts provided by Atlassian to delete inactive workflows and workflow schemes.
    • Standardize and/or Consolidate Similar Workflows
      Standardizing teams around a central way of working will enable you to consolidate similar workflows, but it is a much larger task than simply deleting workflows that are no longer in use. Start by looking at the workflows used by teams that deliver similar types of work. You may find duplicate workflows that can be deleted or workflows with small differences—a step or two—that can be consolidated. There is a balance to achieve here; Jira is designed to be flexible and to meet the needs of different teams. It’s important that teams have a voice in this process to ensure their needs are met.
  • Clean Up and Consolidate Custom Fields
    Having too many custom fields is one of the most common problems we see, and it can have a significant impact on the performance of your Jira instance, particularly around indexing. There are, however, some things you can do to clean up custom fields, including deleting unused or unnecessary ones and consolidating existing ones.
    • Delete Unused and Duplicate Custom Fields
      Jira allows you to analyze custom field use, so that you can determine if any fields have not been used in a long time (or ever), and delete them. Once that’s done, you can check to see if you have duplicate fields — fields with different names that serve the same function—and delete those. Once this has been done, a best practice is to establish nomenclature for common field types across the company and ensure that new custom fields are checked against this list before being added.
    • Address Field Configuration and Context
      Jira also allows you to identify those custom fields that take the longest time to index. From there, you can look at the configuration on the fields to determine if there are ways you can improve it, so it indexes more quickly. You can also look at custom field context—whether it is global or only assigned to specific projects and issues. Custom fields that have been assigned global context but do not require it can then be optimized.

Recommended Reading

Looking to learn more about cleaning up custom fields? Here are two great resources.

          Atlassian: Analyzing the Use of Custom Fields
          Atlassian: Optimizing Custom Fields


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Practical Recommendations for Cleaning Up Confluence

Over time, Confluence is another area where information and data tend to accumulate, making it hard for users to find the most current and/or relevant content and slowing the system down. Confluence cleanup activities fall broadly into two categories: cleaning up your site and spaces, and reducing unnecessary data.

In the following paragraphs, we’ll explore ways to address both concerns.

  • Clean Up Sites and Spaces
    Maintaining a clean, clutter-free Confluence site goes a long way toward enhancing usability — it makes it much easier to find relevant information. Following are three key tactics for reducing clutter related to spaces, pages, and accounts.
    • Delete or Archive Unused Spaces
      If you have old spaces that are no longer in use—personal spaces of people who have left the company, for example—a good way to reduce clutter and minimize impact on system performance is to simply delete them. Depending on your organization’s policies and audit needs, you can also archive them or export them and back them up in long-term storage.
    • Clean Up Unneeded Spaces
      Content often has a shelf life, and after a period of time, you may find that it’s no longer relevant. In addition, people often create duplicate content or start content, then never fully develop it. All of these situations can lead to a cluttered space. There are a couple of options for cleaning up obsolete pages: they can be moved to a specific area of the page tree where they won’t be in the way, or they can be moved to a new space that can then be archived.
    • Disable Accounts Owned by Inactive Users
      Many organizations include disabling accounts owned by inactive users as part of their standard de-provisioning practices, but it is something that occasionally gets overlooked. Similarly, sometimes people change roles and no longer need Confluence access, even though they’re still with the company. It’s worth periodically double-checking to make sure inactive accounts have been disabled.
  • Reduce Unnecessary Data
    Confluence sites can become data heavy, especially if, like many organizations, you are storing iterative versions of multiple files in them. Cleaning up old data may require a bit of manual effort, but it can improve system performance and make backups and upgrades faster. One of the quickest, easiest ways to free up space in Confluence is to simply empty the trash on a regular basis. Beyond that, there are several other tactics at your disposal.
    • Remove Unneeded Large Attachments
      Some users may be storing old, iterative versions of large photo, video, or audio files that are no longer needed because newer versions exist. You can go into Space Attachments and sort by size to see if this is the case. If you find spaces with unusually large attachments, it might be worth it to reach out to the space owner to see if all these are necessary or if some can be deleted.
    • Delete or Export Old Spaces
      Deleting old spaces is not just a way to minimize clutter as we previously described—it can have a big impact on system performance if those spaces house a significant amount of data. If deleting spaces is not an option due to organizational policies or audit concerns, then exporting them and storing them elsewhere will have a similar impact.


Recommended Reading

Looking to learn more about cleaning up Confluence? Here are four great resources.

          Atlassian Support: Clean Up Your Confluence Instance
          Atlassian Support: Delete Confluence Space
Atlassian Support: Archive a Confluence Space
Atlassian Support: Export a Confluence Space

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Best Practices for Maintaining a Clean Atlassian Instance

Since an unwieldy or messy Atlassian instance can have significant impact on system performance and team productivity, maintaining it is a strategic imperative, not a nice-to-have. To ensure that critical maintenance is prioritized, it’s important to have an agreed-upon plan of action in place for how and when to do cleanup-related tasks. Another primary way of maintaining a clean instance is to establish governance around it. This entails setting ground rules for how to use your Atlassian tools, explaining why adhering to the overarching organizational structure is important, and outlining when it is necessary and acceptable to deviate from standards.


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In the following paragraphs, we explore five best practices that will help your organization prioritize and maintain a clean Atlassian instance.

  • Create a Maintenance Plan of Action
    Two key ways of prioritizing cleanup-related activities are to establish metrics that reinforce their business value relative to their impact on work, and to develop a schedule and checklist for what needs to be done and when.
    • Establish Metrics
      Metrics are a data-driven way to help determine when and what to tackle in terms of maintenance. They might include things like the number of projects that haven’t been used in a given time period. Look at ratios such as the number of projects to people, workflows to projects, and/or fields to screens. Unwieldy numbers serve as an indicator that it is time to clean up.
    • Develop a Schedule
      Regularly schedule maintenance in a way that works for the size of your organization and instance, whether that’s quarterly, semiannually, or annually. Make a checklist of what needs to be evaluated and when, and be sure to allocate the appropriate resources and time needed for maintenance.
  • Establish Governance or Guidelines for Using the Tools
    The term governance can be off-putting: it is suggestive of top-down, restrictive rules and regulations, which seemingly contrast with both the flexibility of Atlassian tools and agile practices. Yet, at its core, governance is simply about setting ground rules for how to use your Atlassian tools. There should be an overarching organizational structure and consistent nomenclature that guides decision-making, but thoughtful consideration should also be given to why and when to deviate from the standards that are set.
    • Create a Governance Board or Community of Practice
      Atlassian tools are all about breaking down silos and enabling cross-functional collaboration, and your governance board should reflect this. At Isos Technology, we encourage the notion of a community of practice—a group that represents domain expertise and teams across the company who work together to develop organizational guidelines for tool usage. They should meet frequently to collectively evaluate requests and develop solutions for enabling teams to work in ways that serve them best within the overarching structure.
    • Maintain a Balance between Structure and Flexibility
      Atlassian tools are designed to be flexible and support autonomy among teams in determining how they work, but they’re also intended to support cross-functional collaboration, transparency, and reporting. Because of this, governance is all about maintaining a delicate balance between structure and flexibility.
  • Limit Administrator Access (While Respecting User Needs)
    One of the most straightforward ways to keep your Atlassian instance from getting unwieldy is to limit who has administrator access and can make configuration changes. That said, there is a balance to be achieved—Atlassian tools are designed to be flexible and they need to meet the needs of the teams using them. The best admins are skilled enough to understand organizational strategy around governance while being responsive to team and user needs. They can evaluate requests, think critically about if and how those requests can be standardized, and come up with innovative solutions to meet user needs. In addition, they are forward-looking—they anticipate the upcoming needs of their evolving user base and keep an eye on tool development and enhancement to make sure they are prepared.
  • Turn Your Users into Advocates with Training
    The people who work in your Atlassian tools every day have a vested interest in their success. After all, it’s their work that is impacted if the tools are not working optimally. Once governance and ground rules have been established for how the tools should work, it can be helpful to engage the broader user base in regular training, helping them to understand the why behind the choices, and how they benefit the larger organization. It’s also important to collect feedback. This not only encourages users to become more invested in the tools, it helps them become better stewards of its upkeep and ultimately minimizes downstream cleanup.
  • Engage Experts
    At Isos Technology, we have seen many organizations successfully clean up their Atlassian instances on their own; however, some companies benefit from bringing in an expert. This is particularly true if there are multiple instances, the instance is particularly large, or even if the organization is simply struggling to find the time. An Atlassian Platinum Solution Partner like Isos can help companies build a long-term strategy for how best to use their instances based on business goals, structure their tools so that they can scale effectively without becoming unmanageable, and target the actions that will deliver the greatest return on investment. In addition, Isos brings best practices and know-how around the fastest, most efficient way to get the job done.


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How Isos Technology Can Help

Cleaning up your Atlassian instance is no small undertaking, especially the first time, although the scope and complexity of the task vary widely depending on how large your instance is, how long it has been in use, and what type of resources you have been able to dedicate to its ongoing maintenance. Many organizations attempt to go it alone, to varying degrees of success. If your organization is able to dedicate the human resources and time needed for clean up, then this whitepaper and Atlassian’s cleanup guides are a great place to start. However, if the task seems daunting, if a migration is imminent, or if you simply have not been able to prioritize clean up and maintenance, engaging with a solution partner may be worth it.

Isos Technology is an Atlassian Platinum and Enterprise Solution Partner, and the 2020 Atlassian Partner of the Year: ITSM, and 2019 Atlassian Partner of the Year: Enterprise. Our passion for Atlassian comes from our own experience—one of the first decisions we made as a new company in 2005 was to invest in Atlassian tools to support our own work. From there, the decision to offer support for the tools to our customers was an easy one. Today, our work is 100% focused on helping companies of all sizes, from small-to-medium businesses to large-scale enterprises, get the most return on their technology investment.


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