Atlassian MCP Integration with Claude Completely Stopped Working - Need Help!

[Lee Yung Sheng]

# Atlassian MCP Integration with Claude Completely Stopped Working - Need Help!

**Status:** Seeking Community Help & Reporting Issue

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## Summary

Hello Atlassian Community,

I'm reaching out for help with a critical issue affecting the Atlassian MCP (Model Context Protocol) integration with Claude AI. As of Saturday morning (November 16, 2025), the integration has **completely stopped working** on Claude's remote connector platforms (Claude.ai web and Claude Desktop app), despite working perfectly just 24 hours earlier. Interestingly, the integration still works flawlessly on Claude Code CLI, which suggests this is specifically a remote connector infrastructure issue.

I'm hoping others in the community might have insights, workarounds, or are experiencing similar issues.

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## What Happened

**Timeline:**

- **November 15, 2025**: Everything working perfectly - successfully updated 5 Confluence pages using Claude

- **November 16, 2025 (Saturday morning ~8:00 AM SGT)**: All Claude platforms suddenly unable to execute ANY Atlassian MCP tools

**Current Status:**

- ❌ Claude.ai web browser (Safari & Chrome) - ALL TOOLS FAIL

- ❌ Claude Desktop app - ALL TOOLS FAIL

- ✅ Claude Code CLI (Cursor) - WORKS PERFECTLY

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## Symptoms

### What Works:

- OAuth authentication completes successfully

- "Successfully connected to Atlassian" confirmation appears

- Connection shows as active in Claude's settings

- Tools are recognized and appear in Claude's tool menu

### What Fails:

- **Every single tool execution fails** with generic error: "Error occurred during tool execution"

- Affects all tools:

- Rovo Search (Jira and Confluence)

- Get Confluence spaces

- Get accessible resources

- All other Atlassian MCP operations

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## What I've Already Tried

### Atlassian Admin Configuration ✅

I discovered the new **Domain Access Management** feature for Rovo MCP Server (apparently rolled out Oct 27 - Nov 3, 2025):

**Location:** Atlassian Administration > Apps > AI settings > Rovo MCP server

**Configuration completed:**

- ✅ Enabled "Allow Atlassian supported domains"

- ✅ Manually added `https://claude.ai/**`

- ✅ Manually added `https://claude.com/**`

- ✅ Verified domains appear in "Your domains" list

### Troubleshooting on Claude Side ✅

- ✅ Disconnected and reconnected Atlassian MCP multiple times

- ✅ Cleared browser cache and cookies completely

- ✅ Tested on multiple browsers (Safari and Chrome)

- ✅ Tested on multiple devices (MacBook Pro and Mac Mini)

- ✅ Reinstalled connector from Claude's native marketplace

- ✅ Completed fresh OAuth authentication each time

- ✅ Tested on both Claude.ai web and Claude Desktop app

**Result:** Still fails on all platforms except Claude Code CLI

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## Important Discovery: No Admin Notification

**Question for Admins:** As an Atlassian organization administrator, I don't recall receiving any notification about the domain whitelisting feature being added to Rovo MCP Server.

I only discovered this feature through extensive troubleshooting after the integration broke. I may have missed the notifications, but I didn't see:

- Email notification about the new feature

- In-app notification in Atlassian admin panel

- Warning that existing integrations might be affected

- Migration guide or configuration instructions

**Did other admins receive notifications about this change? I'd like to know if I missed something or if this was a silent rollout.**

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## Questions for the Community

### 1. Is anyone else experiencing this issue?

Particularly after November 15, 2025 - has your Claude integration stopped working?

### 2. Did you receive notification about domain whitelisting?

If you're an Atlassian admin, were you notified about this new feature and the need to configure it?

### 3. Are there any known workarounds?

Besides using Claude Code CLI, has anyone found a way to make the remote connectors work again?

### 4. Is this affecting other AI platforms?

Is this specific to Claude, or are other AI tools using Atlassian's MCP server experiencing similar issues?

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## Technical Details (for those interested)

**Environment:**

- Atlassian Products: Jira Cloud, Confluence Cloud

- Claude Platform: Max plan (personal account)

- Tested on: macOS (latest)

- Browsers: Safari (latest), Chrome (latest)

**Architecture Insight:**

The issue appears to be with Anthropic's remote connector infrastructure. Claude Code CLI works because it uses a local MCP connection with localhost OAuth callbacks, while Claude.ai web and Claude Desktop use Anthropic's cloud proxy to route requests to `mcp.atlassian.com`.

**Error Pattern:**

- OAuth authentication layer: ✅ Works (Anthropic ↔ Atlassian auth succeeds)

- Tool execution layer: ❌ Fails (Anthropic's proxy ↔ Atlassian API calls broken)

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## Temporary Workaround

For anyone facing this issue urgently, the **Claude Code CLI** (available in Cursor and other IDEs) continues to work perfectly. You can use this for Atlassian operations until the remote connector issue is resolved.

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## Additional Resources

**Related Links:**

- Domain Access Settings: [Control Atlassian Rovo MCP server settings](https://support.atlassian.com/security-and-access-policies/docs/control-atlassian-rovo-mcp-server-settings/)

- Supported Domains: [Available Atlassian Rovo MCP server domains](https://support.atlassian.com/security-and-access-policies/docs/available-atlassian-rovo-mcp-server-domains/)

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## Community Help Needed

If you've experienced this issue or have any insights:

- Please share your experience below

- Let me know if you found any workarounds

- Confirm if you're seeing the same symptoms

If you're an Atlassian admin:

- Check if you have the domain whitelisting feature in your admin panel

- Let me know if you received any notification about it

- Share whether your Claude integration is working or not

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Thank you so much for any help or insights you can provide! This integration is critical to our daily workflow, and I'm hoping the community might have solutions or information I've missed.

**Your assistance is greatly appreciated!** 🙏

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**Posted by:** Lee Yung Sheng

**Date:** November 16, 2025

**Status:** UNRESOLVED - Seeking community input