Atlassian Remote MCP Server beta now available for desktop applications

[#1]

Hi everyone, we’re thrilled by the excitement around the Atlassian Remote MCP Server beta that we launched recently. 

Many of you shared the feedback that it would be helpful to be able to use the MCP server from your IDEs or other desktop apps. Our team has been hard at work to address this, and today we're happy to share that we just shipped an update to the MCP server that now allows local clients to connect to it! 

Prerequisites

Connecting to our remote MCP server from a local application requires the following dependencies that are not owned by Atlassian -

• Node.js
• mcp-remote (setup instructions below)

Instructions

Take Claude Desktop as an example, you can find its MCP configuration file from the "Developer" tab in its settings dialog. 

To setup connection to the Atlassian Remote MCP Server beta, you can use the following configuration -

{
  "mcpServers": {
    "atlassian": {
      "command": "npx",
      "args": ["-y", "mcp-remote", "https://mcp.atlassian.com/v1/sse"]
    }
  }
}

Each application's configuration flow for MCP servers can vary, so please follow the instructions from the app you are using as the source of truth. 

Feedback and support

If you have any feedback, suggestions or questions, please visit our support portal here.

[Jay Kelner]

This is great!! Thank you so much for adding localhost support for this.

I was able to get this working with Cursor by adding this to my Cursor mcp.json:

{
  "mcpServers": {

    // ... other mcp servers here

    "atlassian": {
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "https://mcp.atlassian.com/v1/sse"
      ]
    }
  }
}

[Jitendra Vyas]

@Jay Kelner Where did you add Api key?

[Jay Kelner]

@Jitendra Vyas You don't, that's the whole config. mcp-remote prompts you to authenticate in your browser so you don't have to manage an API key. 

[touchapon]

This is great! Is there a way to pass on oauth flow to the frontend app in case the mcp client is running on a cloud server (our backend app)?

[Hector Maldonado]

@Kun Chen I need to use the MCP server for in house corporate application (AB InBev) can you add my exiting oauth client to the white list?

[Alexander Gertz]

@Jay KelnerThanks for your replys.

For anyone wondering how to set it up in Cursor:

you should install mcp-remote with

npm install -g mcp-remote

Also make sure to use a newer version of Node.

Then you can run the command below to trigger the authentication if thats not happening when you try to use the MCP in your IDE.

npx -y mcp-remote https://mcp.atlassian.com/v1/sse

After that you should be able to reload the MCP in Cursor and see the available tools:

Turns out after that I can not use any of these tools in Cursor and the MCP logs does not show exactly what is wrong:

2025-05-15 11:47:14.413 [error] user-atlassian: [50052] [Local→Remote] tools/list

2025-05-15 11:47:14.580 [error] user-atlassian: [50052] [Remote→Local] 1

Nothing shows in the MCP logs after trying to use the Atlassian tools.

[Tom]

Using the mcp-server npx command I can get it working in VS code so that it shows the available tools and calls them.

vs code setup

"mcp": {

"servers": {

"atlassian": {

"command": "npx",

"args": ["-y", "mcp-remote", "https://mcp.atlassian.com/v1/sse"]

 }

 }

 }

But I get this resposne:

{"error":true,"message":"Cloud id: d3b7b7b7-7b7b-7b7b-7b7b-7b...... isn't explicitly granted by the user."}

[Umut Yildirim]

Hey @Kun Chen
I'm from HighlightAI.com we are adding Atlassian as a verified MCP Server but getting this error

The redirect URI is not allowed, the URL is not part of Atlassian whitelisted domains for registered MCP Clients. Redirect URI https://highlightai.com/plugin-deeplink

[Richard Boisvert]

It works now in VS Code, but one tool is causing issues : TransitionJiraIssue. When enabled, I get this in Insider:

Failed to validate tool bb7_transitionJiraIssue: Error: tool parameters array type must have items. Please open a Github issue for the MCP server or extension which provides this tool

[Tom Goodwin]

I'm having some authentication issues. The MCP lauches the authentication dialogue fine, but Accepting gives me a 400 request. I'm definitely logged in to my account, so not sure what is happening. 

Trying this through Cline

[Jitendra Vyas]

Where is the option to allow this MCP to connect with our Jira? My admin is unable to find MCP in the marketplace.

[Song Huang]

 

Got the error after grant the "Altassian MCP" app, what's the reason, permission issue?

UPDATE on 23 May:

Tried with an admin account, and get the error as well. May be it's due to the app also request confluence view/update permission, however, I'm only using Jira now. 

[Bibin Thomas]

for those looking to figure out the cloud-id to use these tools, This would help: https://support.atlassian.com/jira/kb/retrieve-my-atlassian-sites-cloud-id/

EDIT:

I was finally able to get it working on VSCode

My MCP server was:

```

"MCP-Confluence": {

"command": "npx",

"args": [

"-y",

"mcp-remote",

"https://mcp.atlassian.com/v1/sse",

],

}

```

[Robert Bradford]

@Richard Boisvert did you ever find a solution? I'm getting the same error.

[Richard Boisvert]

@Robert Bradford you can just unselect the tool (shift + command + 6 on mac) and it works after, but it is still selected when you exit/reopen VS Code.

[Alex Mansour]

Hey everyone, I keep getting the below errors when trying to use the MCP in VS Code, anyone faced these issues before?

Failed to validate tool ac2_transitionJiraIssue: Error: tool parameters array type must have items

Failed to validate tool bb7_transitionJiraIssue: Error: tool parameters array type must have items

[Manuel Göster]

I have the same issue in vscode using any tool:
Failed to validate tool bb7_transitionJiraIssue: Error: tool parameters array type must have items

[Kate Frett]

I'm seeing the same issue others are seeing when trying to use this MCP server in VS Code. When I issue a general query I see the following error: 

Failed to validate tool bb7_transitionJiraIssue: Error: tool parameters array type must have items

And, when I issue a query like: "call #getConfluencePage 12345" as shown in other comments above, the input is:

{
  "cloudId": "your-cloud-id",
  "pageId": "12345"
}

and the error I see is:

{"error":true,"message":"Cloud id: your-cloud-id isn't explicitly granted by the user."}

It looks like the cloudId is not being set correctly for my MCP server requests. Should this cloudId be set as a part of the mcp-remote operation that performs authentication? Or is this something I need to set manually in my VS Code config (or elsewhere)?

[Christopher Davison]

I was getting the same issue. I had to visit `https://<my-site-name>.atlassian.net/_edge/tenant_info` to get my organizations cloud ID and then tell Claude to remember to always use that when calling out to Atlassian. That seemed to work 

[J_D_ Santen]

you can pick up the cloudId from #getAccessibleAtlassianResources 

for example in vscode / github copilot, for my agent session one of the first prompts for me is:

get my cloudID from #getAccessibleAtlassianResources

then copilot has my cloudId for as long as it stays in context.

[Manuel Göster]

I resolved the bb7_transitionJiraIssue by disabling only this tools. Then you can use all other MCP tools. Looks like it is malconfigured on the atlassian MCP server side!

To disable it, use the Tool icon in your copilot chat window, find it in the list of tools and deselect it.

[malcolm stanley]

How to troubleshoot this or see if there are issues? 
Using with Cursor and a variety of models. 
Yesterday tool calls were responsive. 
Today they appear to go into a black hole. 
No obvious way to see if there is an issue on the Atlassian side,
or to report an issue for support. 
I know it is beta - wondering what the protocol is? 

EDIT - I did open a ticket as suggested up top....

EDIT EDIT - and if course the minute I did it started working again....

[Hiren_trivedi]

Hi @Kun Chen  - could you please suggest how to make the authentication work if using from external tools like n8n ? 

[Zacharya Errafi]

Hello, I'm a Claude subscriber (PRO plan), and I can't manage to configure this "Remote MCP Server" to use it from Claude. Is this normal? I'm not very tech-savvy but I did install npm... what else do I need to do? With this solution I don't have to enter an API Key, right?

I just added this code in the claude_desktop_config.json :

{
"mcpServers": {
"atlassian": {
"command": "npx",
"args": ["-y", "mcp-remote", "https://mcp.atlassian.com/v1/sse"]
}
}
}

[Arjun Otturu]

Hi @Kun Chen , There is no way to restrict the MCP to just have read access from the authorization  page and it seems to always ask for Read and Update/Create access. Will OR Is there be a way to just provide read access ?