Atlassian MCP `autoApprove: true` Not Being Respected

Bug Reports
1

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

Atlassian MCP server configured with autoApprove: true in mcp.json still prompts for permission despite the setting being explicitly enabled. The “Run Everything” Auto-Run Mode also does not apply to the Atlassian MCP tool executions.

Steps to Reproduce

  1. Configure Atlassian MCP server in ~/.cursor/mcp.json with "autoApprove": true as seen below.
  2. Set Auto-Run Mode to “Run Everything” in Cursor settings
  3. Restart Cursor to ensure config is loaded
  4. Attempt to use any Atlassian MCP tool (e.g., search Jira, get Confluence pages)
  5. Observe permission prompt still appears

MCP Configuration (~/.cursor/mcp.json):

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

Expected Behavior

  • With autoApprove: true set in MCP config, Atlassian MCP tools should execute without permission prompts
  • “Run Everything” Auto-Run Mode should apply to MCP tool executions, or at minimum, autoApprove should work independently

Operating System

MacOS

Current Cursor Version (Menu → About Cursor → Copy)

Version: 1.7.54 (Universal)
VSCode Version: 1.99.3
Commit: 5c17eb2968a37f66bc6662f48d6356a100b67be0
Date: 2025-10-21T19:07:38.476Z
Electron: 34.5.8
Chromium: 132.0.6834.210
Node.js: 20.19.1
V8: 13.2.152.41-electron.0
OS: Darwin arm64 24.3.0

Additional Information

Actual Behavior

  • Cursor still prompts: “Run MCP Tool” with options to “Skip”, “Add ‘MCP Tool’ to Allowlist”, or “Run”
  • The autoApprove: true setting appears to have no effect
  • Must manually approve each Atlassian MCP tool execution

Additional Context

  • User is concerned that clicking “Add ‘MCP Tool’ to Allowlist” might change Auto-Run Mode from “Run Everything” to “Use Allowlist”, requiring approval for all other operations
  • Cursor has been fully restarted after config changes
  • JSON syntax has been validated and is correct

Questions

  • Should autoApprove: true in MCP config automatically approve all tool executions from that server?
  • Should “Run Everything” mode apply to MCP tool executions?
  • If neither of these should work, what is the intended way to avoid permission prompts for trusted MCP servers?

Does this stop you from using Cursor

No - Cursor works fine, but has this bug.

2

Hey, thanks for the report. To clarify: autoApprove isn’t supported in mcp.json. Valid fields are: command, args, env, envFile, url, and headers.

The real issue is that “Run Everything” mode isn’t working for MCP tools, this is a known bug affecting many users: MCP Allowlist doesn't work, also can't be edited

Workaround:

This should make “Run Everything” work properly with your Atlassian MCP until the team ships a fix.

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