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Setting Up Auto-Updates with Atlassian via MCP

Connect Jira issues to Key Results and Initiatives for automatic progress tracking. Set up using natural language, track issue counts, completion percentages, story points, or time estimates. Updates daily at 3 AM UTC with read-only Jira access

Updated over 3 weeks ago

Auto-updates from Atlassian eliminate manual data entry by connecting your Jira issue tracking directly to Key Results and Initiatives. Whether you track sprint completion, bug resolution, or feature delivery, Rhythms synchronizes these metrics automatically so your OKRs stay current without copying data.

New to auto-updates? The How to Set Up Auto-Updates article covers the general setup process and when auto-updates work best for your tracking needs.


Before You Connect

Workspace Requirements

Your workspace administrator needs to enable the Atlassian integration in Rhythms before you can connect. Visit Enable Integrations for Your Workspace if you don't see Atlassian as an option.

⚠️ The Atlassian integration requires your workspace to have MCP integrations enabled. If you don't see Atlassian when setting up auto-updates, ask your workspace administrator to enable MCP integrations for your workspace.

Atlassian Admin Configuration

Your Atlassian organization administrator needs to approve domain access in the Atlassian Admin Portal for the connection to work:

  1. Navigate to: AppsAI SettingsRovo MCP Server

  2. Click Add Domain and enter: app.rhythms.ai/* (or your organization's custom Rhythms domain if applicable)

  3. Click Save

This configuration allows all team members in your Atlassian organization to connect their accounts to Rhythms. Your Atlassian administrator can find detailed setup instructions in Atlassian's Rovo MCP documentation.

Access Requirements

You need an Atlassian account with access to the Jira projects and issues you want to track. Rhythms respects your Atlassian permissions:

  • For projects: You need at least view access to the project

  • For issues: You need permission to view the specific issues and their fields

  • For custom fields: You need access to view story points and other custom fields if tracking those metrics

Rhythms only shows you data you can already access in Jira.

What You Can Connect

Rhythms supports numeric Key Results and Initiatives that track measurable progress. Before connecting, make sure your Key Result or Initiative uses a number-based metric rather than milestones or completion status.

What Rhythms Can Track from Jira:

Issue-based tracking: Rhythms tracks issues within projects, epics, or custom JQL queries. You can measure progress through issue counts, completion percentages, or story point totals.

JQL queries: If you use Jira Query Language (JQL) to define specific issue sets (like "all P0 bugs in the Platform project"), Rhythms can track those filtered results. You don't need to write JQL yourself—describe what you want in natural language, and Rhythms generates the appropriate query.

Epic and project hierarchies: Rhythms tracks parent work items (epics, initiatives) and calculates progress based on all child issues. This works well for tracking larger initiatives broken into multiple stories or tasks.


How to Connect Atlassian to a Key Result

Rhythms guides you through Atlassian connections using a conversational interface. You describe what you want to track, and Rhythms locates the data in your accessible Jira projects.

Starting the Connection

  1. Open the Key Result or Initiative you want to connect

  2. Click the More button on the Key Result detail section

  3. Select Set up auto-update

  4. Choose Atlassian from the integration list

  5. Sign in with your Atlassian account if prompted

After authentication, Rhythms starts a conversation to help you find and connect your data.

Guiding Rhythms to Your Data

Tell Rhythms what you want to track in natural language. Rhythms searches your accessible Jira projects, epics, and issues to find matching data.

Example conversations:

"Track completion of the Mobile App Redesign epic in the Design project"

"Monitor P0 bug resolution in the Platform project"

"Count closed customer requests in the Support queue"

"Sum story points for Q1 Engineering sprint"

Rhythms asks clarifying questions if it needs more information:

  • Which project contains the issues?

  • Should it track all issues or specific types (bugs, stories, tasks)?

  • How should progress be calculated (count, percentage, story points)?

  • Are there status or field filters needed?

📝 How Filtering Works: When you describe what to track, Rhythms creates a JQL query that defines your scope. This query runs at setup to identify which issues to track. Once connected, Rhythms tracks those specific issues regardless of how their properties change. For example, if you track "P0 bugs," an issue that was P0 at setup remains tracked even if downgraded to P1 later.

What Rhythms Can Track

Rhythms handles different tracking methods automatically based on your Jira data:

Issue counts: Rhythms counts issues matching your criteria. You can track total issues, completed issues only, or issues with specific statuses. This works well for bug tracking, support tickets, or task completion.

Completion percentages: Rhythms calculates the percentage of "Done" issues out of all issues in scope (0-100%). This approach works best when you want relative progress rather than absolute numbers.

Story points: Rhythms sums story point estimates across issues. If your team uses story points for estimation, this provides a capacity-based view of progress.

⚠️ If story points aren't working as expected, try tracking issue counts or completion percentages instead. Some Jira configurations use non-standard story point fields that Rhythms can't detect automatically.

Time tracking: Rhythms can track original estimates, time spent, remaining estimates, or average progress percentage based on Jira's time tracking fields. This works when your team logs time against issues.

Rhythms recommends the tracking method that best matches your goal's metric and the data available in your issues.

Confirming Your Connection

Before finalizing, Rhythms shows you:

  • The current calculated value

  • The data source (project, epic, or JQL scope)

  • How the value is determined (counting issues, calculating percentage, summing points)

Review this information to confirm Rhythms found the right data. If the value doesn't match your expectations, refine your description and Rhythms will search again.

Once you confirm, Rhythms establishes the auto-update connection and begins daily synchronization.


After You Connect

How Syncing Works

Rhythms updates your Key Result or Initiative daily at 3 AM UTC. Each sync:

  • Retrieves the current value from Jira

  • Updates your progress in Rhythms

  • Maintains your check-in history

What You Still Provide

Auto-updates handle the numbers, but you still create check-ins to provide context. Your check-ins explain progress, highlight blockers, and give stakeholders the story behind the metrics. For guidance on effective check-ins with automated data, see Effective Check-ins to Track OKR Progress in Rhythms.

Seeing Your Connection

After connecting, you'll see a Connected to Atlassian button on your Key Result or Initiative. Click this button to view connection details or disconnect the auto-update.


Current Limitations

The Atlassian integration works well for tracking overall project and epic progress, but has some constraints you should understand before connecting:

What's Not Available Yet

Priority-based filtering: Progress calculations include all child issues under tracked parents. You can use JQL to filter by priority during setup (for example, "priority = P0"), but be aware that if an issue's priority changes after connection, it will still be tracked based on whether it matched the original JQL query. The integration doesn't dynamically re-filter as priorities change.

Time-based metrics: Rhythms can track time estimates and logged hours, but can't track resolution time or age-based metrics (like "Resolve P0 bugs within 48 hours"). For time-sensitive SLA tracking, consider manual check-ins or Jira dashboards, then reference those numbers in your Rhythms check-ins.

Custom field filtering: Progress calculations can't filter by labels, components, tags, or custom fields after the initial JQL scope is set. Use JQL during setup to define which issues to track, but understand that all matching issues contribute to progress calculations.

Issue limits: Each connection can track up to 200 issues. For larger backlogs, use JQL to narrow the scope to your most relevant issues, or consider tracking at a higher level (epic or initiative) rather than individual issues.

In-place editing: To change which issues you're tracking or how progress is calculated, you need to disconnect and reconnect with new criteria. Progress history is preserved during this process, but there will be a gap in automated updates between disconnect and reconnect.

Setup-only availability: The Atlassian integration is available only when setting up auto-updates on Key Results or Initiatives. It's not accessible in general workspace chat after the initial connection is established.

We're evaluating these capabilities for future enhancement. If you have specific filtering needs that would help your team, let us know through the feedback option in your workspace.

Alternatives for Complex Tracking Needs

If you need to track selective subsets with specific filters or time-based metrics, consider:

  • Manual check-ins for precise control over which issues count

  • Jira dashboards with advanced filtering, then reference those numbers in Rhythms check-ins

  • Excel or Power BI for custom calculations pulled from Jira data exports

These alternatives give you complete control over filtering and calculations without the constraints of automated connections.


Adjusting Your Connection

To change your Atlassian configuration, you'll need to disconnect and reconnect. This disconnect-and-reconnect process is the same across all auto-update integrations. Learn more: [LINK: How to Set Up Auto-Updates]

Before you disconnect:

  • Document your current setup (note the project, epic, or JQL scope you're tracking)

  • Verify the data in Jira directly to confirm it matches your expectations

  • Check which issues are included in your current scope

If the numbers look incorrect but the data source selection seems right, first check the Jira data itself. Sometimes unexpected values come from:

  • Issues you didn't realize were included as children of the tracked parent

  • Status categories that don't match your expected "Done" definition

  • Story point fields that aren't populated consistently

  • JQL scope that's broader or narrower than intended

Disconnecting and reconnecting won't fix underlying Jira data issues.

Testing configuration changes:

Before disconnecting your current auto-update, consider testing your new configuration on a separate Key Result. This lets you verify the new data source calculates correctly before switching your primary Key Result.

Create a duplicate Key Result, connect it to Atlassian with your new criteria, and verify the value matches your expectations. Once confirmed, disconnect your original Key Result and reconnect it with the validated configuration.

⚠️ Disconnecting preserves your existing check-in history, but creates a gap in automatic updates until you reconnect. Progress recorded during the gap stays visible, but new automated updates only resume after you establish the new connection.


Frequently Asked Questions

Can I connect multiple Jira projects to different Key Results?

Yes. Each Key Result or Initiative can have its own Atlassian connection, and you can connect different projects, epics, or JQL queries across your Key Results without conflicts.

Can multiple people connect the same Jira epic to different Key Results?

Yes. Multiple team members can connect the same Jira data to different Key Results. Each connection is independent and updates according to each person's Atlassian access permissions. For example, an engineering lead might track overall epic completion while a PM tracks only completed stories.

What happens if I lose access to the Jira project?

If you lose access, Rhythms can no longer retrieve updated values. Your Key Result retains its last known value and check-in history, but automatic updates stop until you regain access or connect a different data source. If updates seem stale, verify you still have the necessary Jira permissions.

Can I connect both Atlassian and another tool to the same Key Result?

No. Each Key Result or Initiative supports one auto-update connection at a time. You can track data from Atlassian or from another integration, but not both simultaneously. To switch tools, disconnect the current integration before setting up the new one.

How often does Rhythms sync with Jira?

Rhythms updates your Key Result daily at 3 AM UTC. This timing ensures your OKR data reflects yesterday's closing numbers each morning. If you need more frequent updates, consider using check-ins to record interim progress manually.

What if my Jira data shows a different value than what appears in Rhythms?

First, verify the Jira data has been updated since the last Rhythms sync (3 AM UTC). If the discrepancy persists:

  • Check that all expected child issues are included in your scope

  • Verify that issue statuses match your "Done" definition

  • Confirm that story points or other custom fields are populated consistently

  • Review whether issues were added or removed from the tracked parent

You can disconnect and reconnect with a new configuration if the scope needs adjustment.

Can I track issues from multiple Jira projects in one Key Result?

Not directly. Each connection tracks data from a single project or JQL query scope. To track across projects, you have two options:

  • Use JQL that spans multiple projects during setup (Rhythms can help you create this)

  • Create separate Key Results for each project, then use an Objective to roll up the combined progress

Does Rhythms modify my Jira issues?

No. Rhythms has read-only access to Jira. It retrieves values to update your OKRs but never writes back to Jira or changes your issues, statuses, or fields.

Can I track priority-based metrics like "Resolve all P0 bugs"?

Yes, but with an important limitation: Rhythms tracks issues based on their properties at setup time, not dynamically.

When you set up tracking for "P0 bugs," Rhythms creates a JQL query (like priority = P0 AND status != Done) that identifies which issues to track. Once connected:

  • ✅ Issues that were P0 at setup remain tracked (even if downgraded to P1 later)

  • ❌ Issues that become P0 after setup are not automatically added to tracking

  • ✅ Progress calculations update daily based on the original set of issues

This means you're tracking "issues that were P0 at the time of setup" rather than "issues that are currently P0."

For active priority-based tracking where you need the set of issues to update as priorities change, consider manual check-ins or Jira dashboard references in your check-ins.

Can I track time-based metrics like "Resolve bugs within 48 hours"?

Not currently. The integration can track time estimates and logged hours, but not resolution time, cycle time, or age-based metrics. Consider manual check-ins with references to Jira dashboard widgets for time-sensitive tracking needs.

Why doesn't my story point total match what I see in Jira?

If story points appear as 0 or don't match your expectations, try these troubleshooting steps:

  1. Check if story points are populated: Verify in Jira that all tracked issues have story point values entered

  2. Try a different tracking method: Switch to issue counts or completion percentages to see if those work correctly

  3. Verify the scope: Make sure all expected issues are included in your tracking scope

Some Jira configurations use non-standard story point fields that Rhythms can't detect automatically. If story points are critical for your tracking and the alternatives don't work, check with your Jira administrator about your organization's story point field configuration.

Can I filter which child issues count toward progress using labels or components?

Yes, but filtering happens at setup time, not dynamically. When you describe what to track, Rhythms creates a JQL query that filters by labels or components. For example, "Track issues labeled 'customer-facing' in the Support project."

Once connected:

  • ✅ Issues with that label at setup remain tracked (even if the label is removed later)

  • ❌ Issues that gain the label after setup are not automatically added to tracking

  • ✅ Progress calculations update daily based on the original set of issues

This means you're tracking "issues that had the label at setup time" rather than "issues that currently have the label."

For dynamic filtering needs where labels or components change frequently, consider manual check-ins or tracking at a different level in your Jira hierarchy (like tracking an epic that naturally contains your desired scope).


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