Top 5 biggest challenges when using Jira for project planning (How to overcome them)

[#1]

Hi community 👋
I’m Asia from TeamBoard.

We’ve just published a new article that explores the top 5 challenges teams face when using Jira for project planning. Let’s take a look at why these challenges happen—and explore practical ways to overcome them

---

Jira is one of the most widely used platforms for managing work, especially for software development and IT teams. It excels at tracking issues, supporting agile workflows, and keeping execution moving forward. However, as organizations grow and projects become more complex, many teams begin to use Jira not just for execution, but also for project planning, coordination, and reporting.

In this article, we explore the 5 biggest challenges teams face when using Jira for project planning and outline practical ways to address them effectively.

Challenge 1: Planning Without Understanding Real Capacity

When managing large projects across multiple teams, it’s easy to assume that assigning work in Jira means it can be completed as planned. Jira shows who a task is assigned to and when it is expected to be done, but it does not reflect whether that person actually has the capacity to take on the work. Technical teams may track progress diligently in Jira, yet project managers and stakeholders lack visibility into availability, competing commitments, or workload constraints.

As a result, plans are often built on assumptions rather than reality. Team members become overloaded without anyone noticing, deadlines slip unexpectedly, and project managers are forced into reactive replanning. These issues are especially common in environments where people contribute to multiple projects, work across time zones, or have varying schedules due to holidays or personal time off.

How to overcome

To handle advanced planning needs that Jira does not support natively, teams can integrate purpose-built plugins from the Atlassian Marketplace. These apps extend Jira’s capabilities without requiring heavy customization or complex configuration.

TeamBoard ProScheduler is one such plugin designed specifically for realistic project and resource planning in Jira. Its visual Schedule Board makes it easy to plan tasks and allocate resources based on actual availability, working hours, roles, and holidays. In addition, the Workload view uses clear color indicators to show who is overloaded or underutilized, allowing project managers to rebalance assignments early and keep delivery plans realistic and sustainable.

Challenge 2: Overwhelming Complexity and Configuration

Jira is known for its flexibility, but without clear governance, that flexibility can quickly turn into complexity. Over time, teams often introduce numerous custom fields, workflows, and schemes to solve specific local needs. While each customization may seem reasonable on its own, the cumulative effect can make Jira difficult to navigate, hard to maintain, and intimidating for non-technical users.

This complexity has a direct impact on project planning and collaboration. New team members face a steep learning curve, onboarding slows down, and inconsistent usage leads to unreliable data. Instead of supporting productivity, Jira can become a system that only a few power users fully understand, limiting its value for broader planning and coordination.

How to overcome

The key to managing complexity is discipline and simplicity. Teams should start with standardized workflows and configurations that can support the majority of projects, customizing only when there is a clear and justified need. Regular audits of custom fields, workflows, and permissions help keep the system clean by removing outdated or redundant configurations before they become a burden.

Challenge 3: Poor Visibility into Dependencies and Delivery Risk

Jira allows teams to link issues using relationships such as “blocks” and “is blocked by,” but these links are largely informational. They don’t actively shape schedules or clearly show how a delay in one task will affect everything that follows. As a result, dependencies often exist in Jira without being fully understood or managed.

This becomes especially problematic in larger projects or cross-team initiatives. A single delayed task can quietly push an entire delivery off track, yet the impact may remain hidden until a key milestone is already at risk—when options are limited and costly.

How to overcome

Teams can use TeamBoard ProScheduler to visualize dependencies and identify blocked work at a higher level. ProScheduler transforms dependencies from passive links into active planning elements by displaying them directly on a timeline and automatically adjusting schedules when work changes. This makes delivery risk visible early, allowing teams to spot fragile parts of the plan and adjust proactively—before deadlines slip.

Challenge 4: Difficulty Visualizing the “Big Picture” (Portfolio Management)

Jira is effective for tracking work at the team level, but it often lacks clear, high-level roadmap visibility for cross-functional initiatives and portfolio planning. When work is spread across multiple projects and teams, it becomes difficult to understand how day-to-day tasks connect to strategic goals or how changes in one initiative impact others. As a result, leadership and program managers may struggle to maintain alignment and make informed decisions.

How to overcome

A strong starting point is structuring Jira issues using a clear hierarchy—such as Initiatives → Epics → Stories → Tasks—to ensure that individual pieces of work roll up into meaningful business objectives. However, structure alone does not provide the full picture needed for portfolio planning.

TeamBoard ProScheduler extends Jira with portfolio-level visibility by bringing multiple projects, initiatives, and timelines into a single, unified schedule. It allows teams to visualize how work aligns over time, understand cross-project dependencies, and see how resources are shared across initiatives. With this big-picture view, organizations can better align execution with strategy, adjust priorities proactively, and communicate progress clearly across the portfolio.

Challenge 5: Inadequate Out-of-the-Box Reporting

 Jira offers a variety of built-in reports and dashboards, but these are often too generic to provide the specific, actionable insights that teams need. While standard reports can show issue counts or sprint progress, they may fall short when it comes to understanding team performance, delivery velocity, or progress toward long-term goals—especially in complex or cross-team environments.

As a result, project managers and stakeholders often struggle to extract meaningful information without additional effort. Important questions require manual analysis, and reporting can become time-consuming and difficult to maintain.

How to overcome

Teams can improve reporting by creating customized dashboards using Jira’s built-in widgets, such as Two-Dimensional Filter Statistics, to track key performance indicators relevant to their goals. In addition, learning to use Jira Query Language (JQL) enables more precise filtering and reporting, allowing teams to tailor views and reports to their specific needs. With well-designed dashboards and effective use of JQL, Jira’s reporting can become far more informative and useful for decision-making.

Conclusion

By understanding these challenges and applying the right practices, whether through better structure, clearer governance, or enhanced planning and reporting approaches, teams can get far more value from Jira. Addressing these gaps helps organizations move from reactive delivery to proactive planning, ensuring that daily work stays aligned with broader goals and that project decisions are based on clear, reliable information.