---
title: "Atlassian MCP Server Setup Guide"
description: "This guide provides step-by-step instructions for configuring the Atlassian MCP (Model Context Protocol) server to enable Claude to interact with Jira and Confluence."
type: skill
canonical_url: https://claudary.paisolsolutions.com/skills/atlassian-mcp-setup
source: "Claudary"
difficulty: intermediate
author: "Claude Code Knowledge Pack"
date: 2026-07-10T11:07:11.006Z
license: CC-BY-4.0
attribution: "Atlassian MCP Server Setup Guide — Claudary (https://claudary.paisolsolutions.com/skills/atlassian-mcp-setup)"
---

# Atlassian MCP Server Setup Guide
This guide provides step-by-step instructions for configuring the Atlassian MCP (Model Context Protocol) server to enable Claude to interact with Jira and Confluence.

## Overview

# Atlassian MCP Server Setup Guide

This guide provides step-by-step instructions for configuring the Atlassian MCP (Model Context Protocol) server to enable Claude to interact with Jira and Confluence.

---

## Table of Contents

- [Prerequisites](#prerequisites)
- [Getting API Tokens](#getting-api-tokens)
- [Environment Setup](#environment-setup)
- [MCP Configuration](#mcp-configuration)
- [Verification](#verification)
- [Troubleshooting](#troubleshooting)
- [Security Considerations](#security-considerations)

---

## Prerequisites

Before setting up the Atlassian MCP server, ensure you have:

1. **Docker installed and running**
   - Verify with: `docker --version`
   - Docker must be able to pull images from `ghcr.io`

2. **Atlassian account access**
   - For Cloud: Account with access to your organization's Jira and Confluence
   - For Server/Data Center: Administrative access to generate personal access tokens

3. **Claude Code CLI installed**
   - The MCP server integrates with Claude Code for AI-assisted workflows

---

## Getting API Tokens

### Atlassian Cloud (Recommended)

API tokens are the standard authentication method for Atlassian Cloud products.

**Step 1: Navigate to API Token Management**

1. Go to [https://id.atlassian.com/manage-profile/security/api-tokens](https://id.atlassian.com/manage-profile/security/api-tokens)
2. Sign in with your Atlassian account

**Step 2: Create a New API Token**

1. Click **Create API token**
2. Enter a descriptive label (e.g., "Claude MCP Integration")
3. Click **Create**
4. **Copy the token immediately** - it will not be shown again

**Step 3: Note Your Credentials**

You will need:
- **Email address**: The email associated with your Atlassian account
- **API token**: The token you just created
- **Instance URL**: Your Atlassian Cloud URL (e.g., `https://yourcompany.atlassian.net`)

**Important:** The same API token works for both Jira and Confluence if they are on the same Atlassian Cloud instance.

---

### Atlassian Server / Data Center

For self-hosted Atlassian products, use Personal Access Tokens (PATs).

**Jira Server/Data Center:**

1. Navigate to your Jira instance
2. Click your profile icon > **Profile**
3. Go to **Personal Access Tokens**
4. Click **Create token**
5. Set token name and expiry
6. Copy the generated token

**Confluence Server/Data Center:**

1. Navigate to your Confluence instance
2. Click your profile icon > **Settings**
3. Go to **Personal Access Tokens**
4. Click **Create token**
5. Set token name and expiry
6. Copy the generated token

---

## Environment Setup

### Step 1: Create Environment File

Create a `.env.local` file in your project root (or the directory where you will run Claude Code):

```bash
touch .env.local
```

### Step 2: Configure Environment Variables

Add the following variables to `.env.local` based on your setup:

**For Atlassian Cloud:**

```bash
# Confluence Cloud Configuration
CONFLUENCE_URL=https://yourcompany.atlassian.net/wiki
CONFLUENCE_USERNAME=your.email@company.com
CONFLUENCE_API_TOKEN=your-api-token-here

# Jira Cloud Configuration
JIRA_URL=https://yourcompany.atlassian.net
JIRA_USERNAME=your.email@company.com
JIRA_API_TOKEN=your-api-token-here

# Optional: Limit to specific spaces/projects
# CONFLUENCE_SPACES_FILTER=DOCS,WIKI,ENG
# JIRA_PROJECTS_FILTER=PROJ,DEV,OPS

# Optional: Enable read-only mode (disables all write operations)
# READ_ONLY_MODE=true
```

**For Atlassian Server/Data Center:**

```bash
# Confluence Server Configuration
CONFLUENCE_URL=https://confluence.yourcompany.com
CONFLUENCE_PERSONAL_TOKEN=your-personal-access-token
CONFLUENCE_SSL_VERIFY=true  # Set to "false" for self-signed certificates

# Jira Server Configuration
JIRA_URL=https://jira.yourcompany.com
JIRA_PERSONAL_TOKEN=your-personal-access-token
JIRA_SSL_VERIFY=true  # Set to "false" for self-signed certificates

# Optional: Limit to specific spaces/projects
# CONFLUENCE_SPACES_FILTER=DOCS,WIKI
# JIRA_PROJECTS_FILTER=PROJ,DEV

# Optional: Enable read-only mode
# READ_ONLY_MODE=true
```

### Step 3: Verify .gitignore

Ensure `.env.local` is in your `.gitignore` to prevent accidental credential exposure:

```bash
# Check if .env.local is ignored
grep -q "\\.env\\.local" .gitignore || echo ".env.local" >> .gitignore
```

---

## MCP Configuration

### Step 1: Create MCP Configuration File

Create or update `.mcp.json` in your project root:

```json
{
  "mcpServers": {
    "atlassian": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "--env-file",
        ".env.local",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ]
    }
  }
}
```

### Step 2: Pull the Docker Image

Pre-pull the image to ensure it is available:

```bash
docker pull ghcr.io/sooperset/mcp-atlassian:latest
```

### Configuration Options

**Multiple Environment Files:**

If you have separate environment files for different purposes:

```json
{
  "mcpServers": {
    "atlassian": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "--env-file",
        ".env.atlassian",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ]
    }
  }
}
```

**Combining with Other MCP Servers:**

```json
{
  "mcpServers": {
    "atlassian": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "--env-file",
        ".env.local",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ]
    },
    "filesystem": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/allowed/dir"]
    }
  }
}
```

---

## Verification

### Step 1: Test Docker Connectivity

Verify the container can start and read your environment:

```bash
docker run --rm --env-file .env.local ghcr.io/sooperset/mcp-atlassian:latest --help
```

### Step 2: Test with Claude Code

Start Claude Code and verify the MCP server is recognized:

```bash
claude
```

Then ask Claude to list available MCP tools or perform a simple operation:

```
List the Jira projects I have access to.
```

Or:

```
Show me the recent pages in Confluence.
```

### Step 3: Verify Specific Operations

**Test Jira connectivity:**
```
What issues are in project [YOUR_PROJECT_KEY]?
```

**Test Confluence connectivity:**
```
List pages in the [YOUR_SPACE_KEY] Confluence space.
```

### Expected Behavior

When working correctly:
- Claude can list Jira projects and issues
- Claude can read and create Confluence pages
- Claude can search across both platforms
- Claude reports any permission errors clearly

---

## Troubleshooting

### Common Issues

**Issue: "Authentication failed" or "401 Unauthorized"**

Causes and solutions:
1. **Invalid API token**: Regenerate your API token from Atlassian
2. **Wrong username**: For Cloud, use your email address, not username
3. **Token expired**: Server/DC tokens may expire; create a new one
4. **Wrong URL format**:
   - Jira Cloud: `https://yourcompany.atlassian.net`
   - Confluence Cloud: `https://yourcompany.atlassian.net/wiki`

**Issue: "Connection refused" or "Cannot reach host"**

Causes and solutions:
1. **Docker networking**: Ensure Docker can reach external URLs
2. **VPN required**: Connect to VPN if accessing internal Atlassian Server
3. **Firewall blocking**: Check corporate firewall rules
4. **Wrong URL**: Verify the URL is accessible in your browser

**Issue: "SSL certificate verify failed"**

For self-signed certificates on Server/Data Center:
```bash
CONFLUENCE_SSL_VERIFY=false
JIRA_SSL_VERIFY=false
```

**Issue: "Permission denied" when reading/writing**

Causes and solutions:
1. **Insufficient permissions**: Your Atlassian account needs appropriate project/space permissions
2. **Read-only mode enabled**: Check if `READ_ONLY_MODE=true` is set
3. **Space/project restrictions**: Verify you have access to the specific space or project

**Issue: Docker image not found**

```bash
# Pull the latest image
docker pull ghcr.io/sooperset/mcp-atlassian:latest

# Verify it exists
docker images | grep mcp-atlassian
```

**Issue: Environment file not found**

Ensure the path in `.mcp.json` is correct:
- Use relative path from where Claude Code runs
- Or use absolute path: `/Users/yourname/project/.env.local`

### Debug Mode

To see detailed logs, run the container manually:

```bash
docker run -it --rm --env-file .env.local ghcr.io/sooperset/mcp-atlassian:latest
```

### Verifying Environment Variables

Check that your environment file is properly formatted:

```bash
# List all variables (redacted)
grep -E "^[A-Z_]+" .env.local | sed 's/=.*/=***/'
```

Expected output:
```
CONFLUENCE_URL=***
CONFLUENCE_USERNAME=***
CONFLUENCE_API_TOKEN=***
JIRA_URL=***
JIRA_USERNAME=***
JIRA_API_TOKEN=***
```

---

## Security Considerations

### Credential Protection

1. **Never commit credentials**: Ensure `.env.local` is in `.gitignore`
2. **Use environment-specific files**: Keep production and development credentials separate
3. **Rotate tokens regularly**: Set calendar reminders to rotate API tokens
4. **Use minimal permissions**: Only grant the Atlassian account permissions it needs

### Read-Only Mode

For safer exploration or demo environments:

```bash
READ_ONLY_MODE=true
```

This prevents any write operations to Jira or Confluence.

### Space and Project Filtering

Limit Claude's access to specific areas:

```bash
# Only access these Confluence spaces
CONFLUENCE_SPACES_FILTER=DOCS,PUBLIC

# Only access these Jira projects
JIRA_PROJECTS_FILTER=SUPPORT,DOCS
```

### Audit Trail

All operations performed through the MCP server are:
- Logged in Atlassian's audit logs
- Associated with your Atlassian account
- Subject to your organization's compliance policies

### Token Revocation

If you suspect a token has been compromised:

1. Go to [Atlassian API Token Management](https://id.atlassian.com/manage-profile/security/api-tokens)
2. Click **Revoke** next to the compromised token
3. Create a new token
4. Update your `.env.local` file

---

## Environment Variable Reference

### Confluence Variables

| Variable | Required | Description |
|----------|----------|-------------|
| `CONFLUENCE_URL` | Yes | Confluence instance URL |
| `CONFLUENCE_USERNAME` | Cloud only | Email address for authentication |
| `CONFLUENCE_API_TOKEN` | Cloud only | API token from Atlassian |
| `CONFLUENCE_PERSONAL_TOKEN` | Server only | Personal access token |
| `CONFLUENCE_SSL_VERIFY` | No | Set to `false` for self-signed certs |
| `CONFLUENCE_SPACES_FILTER` | No | Comma-separated space keys to limit access |

### Jira Variables

| Variable | Required | Description |
|----------|----------|-------------|
| `JIRA_URL` | Yes | Jira instance URL |
| `JIRA_USERNAME` | Cloud only | Email address for authentication |
| `JIRA_API_TOKEN` | Cloud only | API token from Atlassian |
| `JIRA_PERSONAL_TOKEN` | Server only | Personal access token |
| `JIRA_SSL_VERIFY` | No | Set to `false` for self-signed certs |
| `JIRA_PROJECTS_FILTER` | No | Comma-separated project keys to limit access |

### Global Variables

| Variable | Required | Description |
|----------|----------|-------------|
| `READ_ONLY_MODE` | No | Set to `true` to disable all write operations |

---

## Quick Start Checklist

- [ ] Docker installed and running
- [ ] API token created at [Atlassian](https://id.atlassian.com/manage-profile/security/api-tokens)
- [ ] `.env.local` created with credentials
- [ ] `.env.local` added to `.gitignore`
- [ ] `.mcp.json` created with Atlassian configuration
- [ ] Docker image pulled: `docker pull ghcr.io/sooperset/mcp-atlassian:latest`
- [ ] Connection tested with Claude Code

---

## Additional Resources

- [Atlassian API Token Documentation](https://support.atlassian.com/atlassian-account/docs/manage-api-tokens-for-your-atlassian-account/)
- [MCP Atlassian GitHub Repository](https://github.com/sooperset/mcp-atlassian)
- [Workflow Commands Reference](./WORKFLOW_COMMANDS.md) - Commands that use Atlassian integration

---

Source: [Claudary](https://claudary.paisolsolutions.com/skills/atlassian-mcp-setup) · https://claudary.paisolsolutions.com