Atlassian MCP Setup
Configure the Atlassian MCP server to access Jira issues and Confluence pages directly from Claude Code.
When to Use This Skill
Use this skill when:
- •Setting up MCP server integration for Atlassian tools
- •Working with Jira tickets and issues
- •Referencing Confluence documentation
- •Troubleshooting Atlassian MCP connection
Automated Setup Workflow
When this skill is invoked, follow these steps in order:
Step 1: Check if MCP Tools Are Available
Attempt to use an Atlassian MCP tool:
Use: mcp__atlassian__searchJiraIssuesUsingJql
Input: { "jql": "project = TEST" }
- •If successful: MCP is ready. Skip to usage section.
- •If fails with "No such tool available": Continue to Step 2.
Step 2: Check if MCP Server Is Configured
Run check to see server status:
claude mcp list
Possible outcomes:
A) Server not listed:
- •Run configuration script:
bun .claude/skills/atlassian-mcp/configure-mcp.ts - •Instruct user: "The Atlassian MCP server has been configured. Please restart Claude Code with
claude -cto continue this conversation." - •STOP HERE - Wait for user to restart and continue
B) Server listed with "⚠ Needs authentication":
- •Continue to Step 3
C) Server listed with "✓ Connected":
- •MCP should be available but tools aren't loading
- •Instruct user: "Please restart Claude Code with
claude -cto reload MCP servers." - •STOP HERE - Wait for user to restart and continue
D) Server connected but using wrong account:
- •User reports authenticated with wrong Atlassian account
- •Run reauthentication:
bun .claude/skills/atlassian-mcp/configure-mcp.ts --reauth - •Follow reauthentication workflow (see Reauthentication section below)
- •STOP HERE - Wait for user to complete reauth flow
Step 3: Guide Authentication
If server shows "⚠ Needs authentication", provide these instructions:
User must authenticate:
- •Exit Claude Code completely
- •Run in terminal:
claude /mcp - •Select
atlassianfrom the list - •Press Enter to start OAuth flow
- •Complete authentication in browser
- •Restart Claude Code with
claude -cto continue
If authentication fails with admin authorization error:
- •Explain that site admin approval is required (see Troubleshooting section)
- •Provide message template for user to send to admin
- •STOP HERE - Wait for admin approval
Step 4: Verify Connection
After user restarts, repeat Step 1 to verify tools are now available.
Prerequisites
Bun runtime is required. Check with:
which bun
If not installed:
curl -fsSL https://bun.sh/install | bash
Available MCP Tools
Once connected, you'll have access to:
- •
mcp__atlassian__searchJiraIssuesUsingJql- Search Jira using JQL - •
mcp__atlassian__getJiraIssue- Fetch specific Jira issue by key - •
mcp__atlassian__createJiraIssue- Create new Jira issue - •
mcp__atlassian__updateJiraIssue- Update issue fields - •
mcp__atlassian__addJiraIssueComment- Add comment to issue - •
mcp__atlassian__getConfluencePage- Fetch Confluence page - •
mcp__atlassian__searchConfluencePages- Search Confluence
Usage Examples
Search Issues with JQL:
Use mcp__atlassian__searchJiraIssuesUsingJql with JQL query:
Use: mcp__atlassian__searchJiraIssuesUsingJql
Input: {
"jql": "project = PROJ AND status = 'In Progress' ORDER BY updated DESC"
}
Fetch Jira Issue:
Use mcp__atlassian__getJiraIssue with issue key (e.g., PROJ-123):
Use: mcp__atlassian__getJiraIssue
Input: { "issueKey": "PROJ-123" }
Create Jira Issue:
Use: mcp__atlassian__createJiraIssue
Input: {
"projectKey": "PROJ",
"summary": "Implement user authentication",
"description": "Add JWT-based authentication for API endpoints",
"issueType": "Story"
}
Get Confluence Page:
Use mcp__atlassian__getConfluencePage with page ID or URL.
Reauthentication
If you need to switch accounts or reauthenticate with different credentials:
Run reauthentication script:
bun .claude/skills/atlassian-mcp/configure-mcp.ts --reauth
This will:
- •Remove existing MCP server (clears stored OAuth tokens)
- •Reconfigure server with fresh settings
- •Prompt you to authenticate with new credentials
After running reauthentication:
- •Exit Claude Code
- •Run:
claude /mcp - •Select
atlassianand press Enter - •Complete OAuth login with NEW account
- •Restart Claude Code with
claude -c
Use cases:
- •Logged in with wrong Atlassian account
- •Need to switch between multiple Atlassian workspaces
- •OAuth tokens expired or corrupted
- •Testing with different user permissions
Troubleshooting
Admin Authorization Required
If you see: "Your site admin must authorize this app for the site '[organization].atlassian.net'"
Root cause: The Atlassian MCP app requires site admin approval before users can connect. Product admins alone are not sufficient—site admin rights are necessary to approve integrations.
Solution (Site Admin):
- •Log in as Site Admin for [organization].atlassian.net (product admin role is insufficient)
- •Visit Atlassian Admin Console
- •Select your organization/site if you manage more than one
- •Navigate to Apps → AI settings → Rovo MCP server
- •Under "Your domains" section, verify allowed domains are configured
- •Ensure "Allow Atlassian supported domains" is enabled (toggle should be green/checked)
- •If needed, add specific domains under "Your domains" section
- •The Rovo MCP server enables AI tools (like Claude.ai) to connect to Atlassian apps
- •Access scope: View and Update for Jira work data
Solution (User):
Contact your Atlassian site admin (not just product admin) and request they approve "Atlassian MCP" for [organization].atlassian.net.
Message template to send:
Subject: Request to Enable Rovo MCP Server for [organization].atlassian.net Hi [Admin Name], I need access to the Atlassian Rovo MCP server to integrate Jira with Claude.ai development tools. Could you please enable this? Steps: 1. Log in as Site Admin at https://admin.atlassian.com 2. Select [organization].atlassian.net 3. Navigate to Apps → AI settings → Rovo MCP server 4. Ensure "Allow Atlassian supported domains" is enabled (toggle on) 5. Verify domains are configured under "Your domains" section if needed This enables AI tools like Claude.ai to access Jira work data (View and Update permissions). Let me know once enabled. Thanks!
Reference: Atlassian Support - App Authorization Error
MCP Server Shows "Disconnected"
- •Run
claude /mcpin terminal - •Select
atlassian - •Press Enter to trigger OAuth flow
- •Complete authentication in browser
Tools Not Appearing After Restart
- •Verify
~/.claude.jsoncontainsatlassianserver config - •Check OAuth token hasn't expired
- •Re-run authentication flow
Bun Not Found
Install Bun runtime:
curl -fsSL https://bun.sh/install | bash
Related Skills
- •
github-mcp- GitHub MCP integration (token-based) - •
secureai-mcp- SecureAI task management and security controls