Top 3 Mistakes Companies Make in Jira and How to Fix Them

One Question

If your Jira instance is quietly undermining your reporting, automation, and security today, would you actually know where the damage is coming from?

Jira is one of the most powerful tools for project management, yet so many companies fail to leverage its full potential. We recently reviewed a detailed breakdown of some of these top mistakes companies make in Jira, and what struck me is how often the biggest issues hide in plain sight.

Today, we want to focus on the top three mistakes—the ones that most directly undermine reporting, automation, and scalability—and explain why they happen and how to fix them.

Treating Jira as a Simple Task Manager

It’s tempting to use Jira like Trello or Asana: create tasks, move them along a board, and consider the job done. But Jira is far more than a simple task tracker—it’s a process engine.

Companies that treat Jira this way often experience:

• Weak reporting: Without proper issue types, workflows, and field configuration, reporting becomes inaccurate or misleading.

• Inefficient automation: Automations depend on well-defined processes. If your Jira instance is just “task lists everywhere,” automations fail or create chaos.

• Poor scalability: What works for a team of five rarely works for an enterprise with hundreds of users.

  
  

The fix:  

• Define Jira as a process-driven system. Map your workflows to actual business processes.

• Train teams on the strategic use of issue types, boards, and filters.

• Audit your reporting regularly to ensure data integrity.

Over-Usage of Custom Fields

Custom fields are a double-edged sword. They can make Jira flexible, but when overused or mismanaged, they lead to:

• Performance issues: Each custom field adds complexity to Jira’s database, slowing down operations.

• System instability: Unused or redundant fields can cause bugs or unexpected behavior.

• Maintenance headaches: Administrators spend hours cleaning up fields instead of delivering business value.

Why it happens: Teams often add fields for every “nice-to-have” request without auditing existing fields or considering alternatives.

The fix:  

• Conduct a custom field audit every 6–12 months.

• Remove unused or redundant fields.

• Standardize field usage across projects to reduce chaos.

Broken Permission Schemes

Permissions are the backbone of a secure and well-governed Jira instance. Yet many companies:

• Grant everyone admin rights.

• Leave projects viewable to all logged-in users.

• Fail to define clear admin roles for projects.

  
  

The consequences are severe:

• Security risks: Unauthorized changes can compromise data integrity.

• Mismanagement: Without defined roles, Jira administrators can inadvertently disrupt workflows or automation rules.

• Compliance gaps: Companies in regulated industries risk audits and penalties.

The fix:  

• Define clear roles and responsibilities for system and project administrators.

• Regularly review permission schemes to ensure minimal access required for tasks.

• Implement a governance model to manage exceptions and escalations.

These three mistakes alone can drastically undermine the ROI of your Jira implementation.

Your Turn: We’d love to hear from you, what’s the most common Jira mistake you’ve seen in real life? Drop a comment below and share your experience.