Setting Up Auto-Updates with Atlassian via MCP

Last updated: June 11, 2026

Connect Jira and Confluence to Rhythms for automatic OKR progress tracking and conversational Atlassian operations. Track issue counts, completion percentages, story points, or time estimates — and go further by creating issues, transitioning statuses, updating Confluence pages, and more, all from the Rhythms chat interface.

The Atlassian MCP integration gives you two distinct capabilities: auto-updates that keep your Key Results and Initiatives in sync with Jira data automatically, and chat-driven operations that let you work with Jira and Confluence conversationally without leaving Rhythms.

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. Visit the Atlassian Admin Portal

  2. Navigate to: Apps → AI Settings → Rovo MCP Server

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

  4. 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, issues, and Confluence spaces you want to work with. Rhythms respects your Atlassian permissions:

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

  • For Jira issues: You need permission to view, and where applicable, edit or transition the specific issues

  • For Confluence: You need view access to spaces and pages; write access is required to create or update pages and add comments

  • 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 Atlassian, and only performs write operations you have permission to execute.

What You Can Connect for Auto-Updates

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.

Setting Up Auto-Updates from Jira

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, whether to track all issues or specific types, how progress should be calculated, and whether status or field filters are 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 from Jira

Issue counts: Rhythms counts issues matching your criteria — total issues, completed issues only, or issues with specific statuses. 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%). Best when you want relative progress rather than absolute numbers.

Story points: Rhythms sums story point estimates across issues. Provides a capacity-based view of progress when your team uses story points for estimation.

⚠ 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.

JQL queries: If you use Jira Query Language to define specific issue sets, 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. Works well for tracking larger initiatives broken into multiple stories or tasks.

Confirming Your Connection

Before finalizing, Rhythms shows you the current calculated value, the data source (project, epic, or JQL scope), and how the value is determined. Review this 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.

What Else You Can Do with Atlassian in Rhythms Chat

Beyond auto-updates, the Atlassian integration is available throughout the Rhythms chat interface. You can ask Rhythms to perform Jira and Confluence operations conversationally — no need to switch tabs or context.

Jira Operations

Search and read:

  • Search issues using natural language or JQL

  • Look up specific issues, view their details, comments, and linked issues

  • Browse visible projects and issue types

Create and edit:

  • Create new Jira issues with title, description, type, assignee, and priority

  • Edit existing issues — update fields, descriptions, and assignments

  • Create links between issues (e.g., "blocks", "is blocked by", "relates to")

Move work forward:

  • Transition issues to a new status (e.g., move a bug from "In Progress" to "Done")

  • Add comments to issues to document decisions or updates

  • Log work against issues

Example prompts:

  • "Create a Jira bug in the Platform project for the login timeout issue"

  • "Move RHY-142 to In Review"

  • "Add a comment to ENG-88 saying the fix is deployed to staging"

  • "Search for all open P0 issues assigned to me in the Mobile project"

  • "Link RHY-200 as blocking RHY-201"

Confluence Operations

Search and read:

  • Search Confluence pages using CQL or natural language

  • Read page content, view page hierarchies and descendants

  • Browse spaces and list pages within a space

  • Read inline and footer comments on pages

Create and update:

  • Create new Confluence pages in any space you have write access to

  • Update existing pages with new content

  • Add inline comments (anchored to specific text) or footer comments to pages

Example prompts:

  • "Find the Q2 Engineering planning page in Confluence"

  • "Create a Confluence page in the Product space summarizing this week's OKR check-ins"

  • "Update the Release Notes page with the changes we shipped this sprint"

  • "Add a comment to the Architecture Decision Record page flagging the open question about auth"

After You Connect Auto-Updates

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, and 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

Auto-Update Limitations

Priority-based filtering: Progress calculations include all child issues under tracked parents. You can use JQL to filter by priority during setup, but 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.

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

Adjusting Your Connection

To change your Atlassian auto-update configuration, you'll need to disconnect and reconnect. Learn more: 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

Testing configuration changes: Before disconnecting your current auto-update, consider testing your new configuration on a separate 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.

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.

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.

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. To switch tools, disconnect the current integration before setting up the new one.

How often does Rhythms sync with Jira for auto-updates? Rhythms updates your Key Result daily at 3 AM UTC. If you need more frequent updates, consider using check-ins to record interim progress manually.

Does Rhythms modify my Jira issues during auto-updates? No. Auto-updates are read-only — Rhythms retrieves values from Jira to sync your OKR progress but never writes back to Jira during automated syncs.

However, through the Rhythms chat interface, you can ask Rhythms to create issues, edit issues, transition statuses, add comments, and log work in Jira. These are explicit actions you initiate in chat, not automated background operations.

Can I use Rhythms to work with Confluence? Yes. Through the Rhythms chat interface, you can search Confluence pages, create new pages, update existing pages, and add inline or footer comments — in any Confluence space you have access to. See the What Else You Can Do with Atlassian in Rhythms Chat section above for examples.

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, and review whether issues were added or removed from the tracked parent.

Can I track issues from multiple Jira projects in one Key Result? Not directly via a single auto-update connection. To track across projects, use JQL that spans multiple projects during setup (Rhythms can help you create this), or create separate Key Results for each project and use an Objective to roll up the combined progress.

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 that identifies which issues to track at that moment. Issues that become P0 after setup are not automatically added to tracking.

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.

Can I track time-based metrics like "Resolve bugs within 48 hours"? Not currently for auto-updates. 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? Check that all tracked issues have story point values entered, try switching to issue counts or completion percentages to see if those work correctly, and verify that all expected issues are included in your tracking scope. Some Jira configurations use non-standard story point fields that Rhythms can't detect automatically.

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

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