All 30+ tools are listed and visible in the settings panel
Tools work when invoked manually through Cursor’s chat UI
Problem:
Tools are NOT exposed to the programmatic agent API layer (CallMcpTool)
When the AI agent attempts to call any tool (e.g., getConfluencePage, updateConfluencePage, atlassianUserInfo), it returns: “Tool {server}-{toolName} was not found”
The tool descriptor JSON files ARE written to the MCP cache folder (mcps/project-0-dataq-Atlassian-MCP-Server/tools/), confirming Cursor detects the tools, but they are not registered in the agent runtime
I asked Atlassian and they said:
Until Cursor updates their MCP integration to surface those tools to agents, there isn’t a true “fix” on your side.
Can you help?
Steps to Reproduce
Add an HTTP-based MCP server to .cursor/mcp.json
Restart Cursor
Complete the OAuth authentication flow in the browser when prompted
Confirm the server shows green/connected in Settings > MCP Servers, with tools listed
Open Agent mode (Cmd+I or the agent panel)
Ask the agent to call any Atlassian MCP tool, e.g.: “Use the Atlassian MCP server to get my user info” or “Get the Confluence page with ID 12345”
The agent attempts CallMcpTool with server project-0-dataq-Atlassian-MCP-Server and tool name atlassianUserInfo
Error returned: “Tool project-0-dataq-Atlassian-MCP-Server-atlassianUserInfo was not found”
Expected Behavior
Tools registered by HTTP-based MCP servers (using the “url” config format) should be callable by the AI agent through CallMcpTool, just like tools from stdio-based MCP servers (using “command” + “args” config format). The agent should be able to invoke updateConfluencePage, getConfluencePage, etc. programmatically.
Operating System
Windows 10/11
Version Information
Cursor 0.48.x (Build 2.5.17)
VS Code base 1.108.0
OS Windows 10 (NT 10.0.26100)
Architecture x64
Node.js v22.17.0
MCP Server Atlassian Rovo MCP (HTTP, https://mcp.atlassian.com/v1/mcp)
Hey, thanks for the detailed report. This is a known issue: MCP tools show up in settings and work in chat, but the agent can’t call them via CallMcpTool.
A few things to try:
New session workaround: open a new chat in Agent mode and first ask, “list all MCP tools you have access to”. After that, the agent may start using tools in that session.
HTTP compatibility mode: go to Settings > Network > HTTP Compatibility Mode, switch to http/1.1, restart Cursor, and try again in a new chat. Some users said this fixed it.
Can you share:
The Request ID from the broken chat (three dots in the top right > Copy Request ID)
Your exact mcp.json config (you can redact secrets)
The team is aware of this category of issues. Your report helps with prioritization, especially since you’re on the latest version, which may mean a previous fix didn’t fully cover HTTP-based (URL config) servers.
I have same issue. After a recent Cursor upgrade maybe 2.5.x, I cannot get chat to use Atlassian MCP. I’ve tried explicitly referencing it many ways and it doesn’t work. I’ve reinstalled MCP and authenticated again.
After the recent update 2.5.17 my Agents lost access to Atlassian MCP and Asana MCP. After switching HTTP compatibility back to http/1.1 it started to work again.
Glad it helped. The Request ID from the broken chat would be useful, if you still have it, send it over. But if you already closed that chat, no worries.
