Jira Issues and Confluence Pages with Atlassian MCP and Continue
Use Continue and the Atlassian Rovo MCP to search, summarize, and manage Jira issues, Confluence pages, and Compass components with natural language prompts.
What You'll Build
An Atlassian workflow assistant that uses Continue with the Atlassian Rovo MCP to:
- Search and summarize Jira issues across projects
- Find and digest Confluence documentation
- Create and update Jira issues with natural language
- Query Compass components and service dependencies
- Automate Atlassian workflows with headless CLI runs
The new Atlassian Mission Control Integration enables Continuous AI for project management and documentation - where AI agents autonomously manage Jira issues, sync Confluence documentation, and streamline development workflows. This cookbook focuses on CLI-based workflows, but you can also deploy autonomous agents through Mission Control.
Get Started: Use this cookbook to understand Atlassian MCP fundamentals, then enable Mission Control to deploy autonomous project management agents across your organization.
Prerequisites
Before starting, ensure you have:
- Continue account with Hub access
- Node.js 18+ installed locally
- An Atlassian Cloud site with Jira, Confluence, and/or Compass
- Access to the Atlassian products you want to integrate with
The Atlassian Rovo MCP Server is currently in Beta. Core functionality is available, but some features are still under development.
For all options, first:
1
Install Continue CLI
curl -fsSL https://raw.githubusercontent.com/continuedev/continue/main/extensions/cli/scripts/install.sh | bash
2
Understand OAuth Flow
The Atlassian MCP uses OAuth 2.1 for authentication. The first time you connect, you'll complete a browser-based authorization flow that respects your existing Atlassian permissions.
To use agents in headless mode, you need a Continue API key.
All data access respects your existing Jira, Confluence, and Compass user permissions.
Choose Your Atlassian Agent
🚀 Two Specialized Agents
We've created two ready-to-use agents to help you get started fast - they come pre-configured with optimized prompts, rules, and the Atlassian MCP. You don't have to use these agents, but they're designed to give you the best experience right away. Choose the agent that matches your needs, or create your own custom agent.
Agent Quick Reference
| Agent | Best For | Use Cases | Link |
|---|---|---|---|
| Jira Agent | Issue Management | Search issues, create stories, sprint planning, status updates, bulk operations | View Agent |
| Confluence Agent | Documentation | Search pages, summarize docs, create/update pages, manage spaces | View Agent |
Cross-product workflows: Both agents can work with Jira, Confluence, and Compass. Choose based on your primary focus area, or create your own agent using the Atlassian MCP. The Atlassian MCP can work with Jira, Compass, or Confluence.
1
Use the Jira Agent
Visit the Atlassian Continuous AI - Jira Agent on Continue Mission Control. This agent is optimized for:
- Searching and filtering Jira issues
- Creating and updating issues
- Sprint planning and workload analysis
- Issue transitions and status updates
No installation needed - you can start using it immediately from the command line!
2
Complete OAuth Authorization
On first use, you'll be prompted to authorize the MCP server in your browser. This is a one-time setup that grants access based on your Atlassian permissions.
3
Run Your First Command
From anywhere in your terminal:
cn --agent continuedev/atlassian-continuous-ai-jira-agent "Show me my open issues assigned to me"
The agent will connect to your Atlassian site and return results.
Pro tip: Create a shell alias for the Jira agent:
alias jira-ai='cn --agent continuedev/atlassian-continuous-ai-jira-agent'
Then use:
jira-ai "your prompt"Jira Workflows
Using the Jira Agent: All examples below use the Jira Agent which is optimized for issue management.
Use natural language to explore, triage, and manage Jira issues. The agent calls Atlassian MCP tools under the hood.
Running in headless mode: Add
-p flag before your prompt and --auto flag at the end:cn --agent continuedev/atlassian-continuous-ai-jira-agent -p "your prompt" --auto
Important: Complete browser OAuth authentication first before using headless mode.
Search and Discovery
Create and Update
Confluence Workflows
Using the Confluence Agent: All examples below use the Confluence Agent which is optimized for documentation management.
Access, search, and manage your team's documentation directly from Continue.
Running in headless mode: Add
-p flag before your prompt and --auto flag at the end:cn --agent continuedev/atlassian-continuous-ai-confluence-agent -p "your prompt" --auto
Important: Complete browser OAuth authentication first before using headless mode.
Search and Summarize
Create and Update
Compass Workflows
Using Either Agent: Compass workflows work with both agents. Use the Jira agent for component-to-issue workflows, or the Confluence agent for component-to-docs workflows.
Query and manage your service architecture with Compass integration.
Running in headless mode: Add
-p flag before your prompt and --auto flag at the end. Complete browser OAuth authentication first before using headless mode.Service Discovery
Combined Workflows
Cross-Product Workflows: These workflows span multiple Atlassian products. Choose the agent based on your primary focus:
- Use Jira Agent when the workflow is issue-centric
- Use Confluence Agent when the workflow is documentation-centric
Integrate actions across Jira, Confluence, and Compass for powerful cross-product workflows.
Running in headless mode: Add
-p flag before your prompt and --auto flag at the end. Complete browser OAuth authentication first before using headless mode.Troubleshooting
Admin Considerations
For Atlassian Site Admins
Installation: The Atlassian Rovo MCP is automatically installed on first OAuth authorization (JIT installation) - no Marketplace installation needed.
Managing Access:
- View connected apps in Admin Hub
- Users can revoke access from their profile settings
- Block user-installed apps via "user-installed apps" control in Admin Hub
Security: All traffic is encrypted via HTTPS (TLS 1.2+), and access respects existing user permissions.
What You've Built
After completing this guide, you have a complete AI-powered Atlassian workflow system that:
- ✅ Uses natural language — Simple prompts for complex Atlassian operations
- ✅ Spans multiple products — Seamlessly works across Jira, Confluence, and Compass
- ✅ Respects permissions — Secure OAuth-based access with existing role enforcement
- ✅ Runs headlessly — Integrate into CI/CD pipelines and automation scripts
Continuous AI
Your Atlassian workflows now operate at Level 2 Continuous
AI -
AI handles routine project management tasks with human oversight through
review and approval.
Next Steps
- Explore your projects - Try the Jira search and triage prompts
- Organize documentation - Use Confluence workflows to summarize and create pages
- Map your services - Query Compass for service dependencies
- Customize prompts - Tailor workflows to your team's specific needs
- Monitor usage - Track how AI improves your Atlassian workflows
Additional Resources
Atlassian Rovo MCP
Official Atlassian MCP documentation
MCP in Continue
How MCP works with Continue agents
Continue Mission Control
Create and manage your agents
Atlassian Community
Get help and share feedback
Example Use Cases
Release Management
Automate release notes generation, link issues to documentation, and track deployment status across Jira and Confluence.
Sprint Planning
Analyze workload distribution, identify blockers, and generate sprint summaries automatically.
Service Ownership
Map service dependencies in Compass, link to technical documentation in Confluence, and track related issues in Jira.
Onboarding Automation
Create standardized Jira onboarding tickets, link to Confluence guides, and track new hire progress.