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

Yung
Yung
Contributor
November 15, 2025
# Atlassian MCP Integration with Claude Completely Stopped Working - Need Help!

 

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

 

---

 

## 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.

 

---

 

## 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

 

---

 

## 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

 

---

 

## 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

 

---

 

## 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.**

 

---

 

## 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?

 

---

 

## 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)

 

---

 

## 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.

 

---

 

## 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/)

 

---

 

## 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

 

---

 

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!** 🙏

 

---

 

**Posted by:** Lee Yung Sheng
**Date:** November 16, 2025
**Status:** UNRESOLVED - Seeking community input
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Yung
Yung
Contributor
November 16, 2025

I have spent another hour doing detailed investigations. 

Atlassian Support has suggested that I ask the community at Atlassian MCP Server group where the product manager is the moderator. This discussion is now moved to https://community.atlassian.com/forums/Atlassian-Remote-MCP-Server/Atlassian-Rovo-MCP-Claude-Web-Desktop-Suddenly-Failing-Anyone/td-p/3147796. 

Atlassian Support says that they can't provide official support since it Atlassian MCP is in Beta mode. If you are experiencing issues. Please submit feedback to https://customerfeedback.atlassian.net/servicedesk/customer/portal/1701/group/1762/create/11360 in the hope that more messages to them will get them to fix it sooner than later. 

 

On 17 November 2025 at 4:17:13 AM, Matt Hogben (jirastudio-support-system@atlassiansupport.atlassian.net) wrote:

—-—-—-—

Matt Hogben commented:

Hello Lee,

I hope you are doing well, and thank you for contacting Atlassian today. My name is Matt and I'll be assisting you with this case.

In this case the Atlassian MCP server is still in beta so it is not supported by Atlassian support. You can reach out directly to the developers for support throughout the beta as they are the experts on the MCP server.

You can reach them directly on the support portal here.

You may also want to report your issue on Atlassian Rovo MCP Server, which has active members who may have also experienced similar situations and can provide helpful assistance.

Thanks again Lee, and I look forward to hearing back from you. If you do have any additional questions please don't hesitate to reach out and I'll be happy to assist.

Kind regards,
Matt
Senior Support Engineer, Enterprise Cloud
Standard Business Hours: 9:00 am - 5:00 pm AEST (GMT +10)

 

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Yung
Yung
Contributor
November 17, 2025

This discussion is moved to the new thread which is hosted by the Product Manager of Atlassian Rovo MCP. There is nothing a user can do to fix the issue. The diagnosis is clear. Claude rolled out something on Fri/Sat that broke the MCP integration with SSE. They have to fix it.

It is now fixed and Claude is working again with Atlassian Rovo MCP. You do not need to do anything. This was a server side issue.

There is no use raising the issue with Claude support. They have always been unresponsive to me even as a Claude Max subscriber. As of now, they have not replied to my support message raised 36 hours ago.

Atlassian Support is much more responsive and proactive. They have confirmed that Atlassian MCP could work with Cursor (24 hours ago) and it is a Claude server side issue.

--

Dilip Venkatesh commented:

Dear Customer,

**Update: Issue Resolved**

We're pleased to inform you that the integration issues have been resolved. You should now be able to use the Atlassian MCP with Claude Web and Desktop without encountering errors.

**Next Steps:**

* Please reconnect to the integration and test your workflows
* If you continue to experience any issues, please reach out to us immediately with specific details

**Technical Details:**

We've conducted a thorough investigation and confirmed that no changes or regressions occurred on the Atlassian side regarding SSE (Server-Sent Events) support. We're actively collaborating with Anthropic (Claude) to identify the root cause and implement preventative measures to ensure service reliability going forward.

**We Appreciate Your Patience**

Best regards,
Atlassian MCP Platform Team

---

This request is now completed.

Dilip Venkatesh changed the status to *Done.*

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Kostya Vlasenko
Kostya Vlasenko
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November 17, 2025

Issue is still there, so not sure why it marked as solved here 

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Yung
Yung
Contributor
November 17, 2025

It’s marked as solved to point u to the new post in the product group that is monitored by Atlassian Rovo MCP beta engineering team. The updated status and detailed tech discussions are in that thread. This thread is closed and nit updated by me. 

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Himmet
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November 17, 2025

Yes, I was also excited for the solution. But the accepted answer just invites the readers to complain at that given link to increase its priority. 

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Yung
Yung
Contributor
November 17, 2025

If you read the new discussion thread. You will see that we have confirmed with Atlassian support that the issue is with Claude rolling out something that broke the SSE mcp integration. The new thread is in the product mcp group which is hosted by the product manager of Atlassian mcp. There is no value in talking about it in thi thread that is not monitored by Atlassian product mgt. We have to do it in other thread. There is nothing that Atlassian or user can do until Claude fixes their server. They rolled out something that broke the integration last Fri/ Sat. 
claude is working now with Atlassian. You don’t have to do anything. The diagnosis was clear that it’s an issue with Claude backend server. 

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November 17, 2025

Thanks for clarifying and your contribution in resolving this matter. 

I can also confirm that it is working again. I believe this thread still received traction due to its recency which favored its listing on google search.

So it was a good solution to gesture at the correct thread. 

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Yung
Yung
Contributor
November 17, 2025

I have updated the official response from Atlassian Support confirming that it is working again, and your notification that it is working for you is an additional validation. I have updated the Atlassian Support response on both threads to close out this issue.

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Ilya Alexandrov
Ilya Alexandrov
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November 17, 2025

Having the same issue since 16.11

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Prasanjit Singh
Prasanjit Singh
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November 16, 2025

Having the same issue since yesterday!

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Himmet
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November 16, 2025

@Yung  I highly appreciate your indepth explanation of this frustrating malfunction.

The problem is indeed on Atlassians side.

The Claude Code CLI is really cumbersome, but still better than navigating the horrible UI of Jira. 

My apologies for my my bitter mood, I just did not expect such a lengthy troubleshooting that would eat away my weekend.

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Yung
Yung
Contributor
November 16, 2025

I'm quite frustrated as well. I spent about four hours doing a deep analysis, restarting the browser, logging out, disconnecting and reconnecting the Atlassian MCP, troubleshooting every single component, before coming to the conclusion that it was due to the Atlassian whitelisting that had blocked out Claude.ai and Claude desktop.

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Yossi Golan
Yossi Golan
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November 16, 2025

Thanks - Having the exact same issue as well.

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Yung
Yung
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November 16, 2025

Guess we're in the same boat.

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Ian
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November 16, 2025

@Yung

Thanks for documenting what you've found and done.

  1. Yes, I'm experiencing the same issue. 
  2. I did not receive the notification you asked about.
  3. I don't know of any workarounds beyond what you mentioned 
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Yung
Yung
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November 16, 2025

Thanks for letting me know.

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