MCP server env vars from .mcp.json not passed to spawned process

Status Fixed / completed

Maintainer reply None cached

Activity 5 comments · opened Feb 2, 2026 · closed Feb 2, 2026

Description

Environment variables defined in .mcp.json under a server's env key are not being passed to the spawned MCP server process. This means MCP servers that depend on env-based configuration (like @modelcontextprotocol/server-memory with MEMORY_FILE_PATH) silently fall back to defaults.

Steps to Reproduce

Create .mcp.json in a project root:

{
  "mcpServers": {
    "memory": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-memory"],
      "env": {
        "MEMORY_FILE_PATH": "/Users/me/.claude-memory/memory.json"
      }
    }
  }
}

Start a Claude Code session in that project directory
Use a memory MCP tool (e.g., mcp__memory__search_nodes)
Inspect the spawned mcp-server-memory process environment:

ps eww -p <PID> | grep MEMORY_FILE_PATH

Expected Behavior

The process should have MEMORY_FILE_PATH=/Users/me/.claude-memory/memory.json in its environment, and the MCP memory server should read/write to that file.

Actual Behavior

MEMORY_FILE_PATH is not set on the spawned process (confirmed via ps eww)
The server uses an ephemeral in-memory store instead of the configured file
Data written via Claude Code's MCP tools is lost on server restart
The same .mcp.json env config works correctly when used by Claude Desktop via claude_desktop_config.json

Diagnostic Evidence

# Claude Desktop's server (PID from Claude.app) — env var present:
MEMORY_FILE_PATH=/Users/me/.claude-memory/memory.json

# Claude Code's server (PID from npx) — env var missing:
MEMORY_FILE_PATH not set

Both servers use identical config ("env": {"MEMORY_FILE_PATH": "..."}) — only the Claude Code spawner fails to pass it through.

Impact

MCP servers that rely on env vars for configuration silently malfunction
No error or warning is shown — the server starts fine but with wrong config
For server-memory specifically: knowledge graph data is not persisted and not shared with Claude Desktop, defeating the purpose of a shared memory store

Environment

macOS (Darwin 25.2.0, arm64)
Claude Code (latest as of 2026-02-02)
@modelcontextprotocol/server-memory via npx
.mcp.json in project root

View original on GitHub ↗

5 Comments

edumusikse · 8 months ago

Additional Finding: User-scope config also affected

Tried moving the MCP server config from project scope (.mcp.json) to user scope via claude mcp add -e MEMORY_FILE_PATH=... -s user:

$ claude mcp get memory
memory:
  Scope: User config (available in all your projects)
  Status: ✓ Connected
  Type: stdio
  Command: npx
  Args: -y @modelcontextprotocol/server-memory
  Environment:
    MEMORY_FILE_PATH=/Users/stephan/.claude-memory/memory.json

The config shows correctly with the env var listed. However, the already-running server process in this session still doesn't have the env var:

$ ps eww -p <PID> | grep MEMORY_FILE_PATH
# (empty — not set)

This needs a fresh Claude Code session to test properly. Will update after restarting Claude Code to confirm whether user-scope config correctly passes env vars on fresh session start.

The claude mcp get output confirms Claude Code knows about the env var — the question is whether it passes it to the spawned process.

github-actions[bot] · 8 months ago

Found 3 possible duplicate issues:

This issue will be automatically closed as a duplicate in 3 days.

If your issue is a duplicate, please close it and 👍 the existing issue instead
To prevent auto-closure, add a comment or 👎 this comment

🤖 Generated with Claude Code

edumusikse · 8 months ago

Workaround Found

The @modelcontextprotocol/server-memory has a default fallback path when MEMORY_FILE_PATH is not set:

// From dist/index.js
export const defaultMemoryPath = path.join(
  path.dirname(fileURLToPath(import.meta.url)), 
  'memory.jsonl'
);

This resolves to: ~/.npm/_npx/<hash>/node_modules/@modelcontextprotocol/server-memory/dist/memory.jsonl

Workaround: Symlink the default fallback file to the actual shared memory file:

# Find the default file
DEFAULT_PATH=$(find ~/.npm/_npx -path "*/server-memory/dist/memory.jsonl" 2>/dev/null | head -1)

# Replace with symlink to shared memory file  
rm "$DEFAULT_PATH"
ln -s ~/.claude-memory/memory.json "$DEFAULT_PATH"

This makes Claude Code's memory server read/write the same file as Claude Desktop, even though the env var isn't being passed.

Limitation: The symlink breaks whenever npx refreshes its cache for @modelcontextprotocol/server-memory, since the entire _npx/<hash>/ directory gets recreated. Needs periodic re-symlinking.

The underlying bug remains: Claude Code should be passing env vars from .mcp.json to spawned MCP server processes, matching Claude Desktop's behavior.

edumusikse · 8 months ago

Closing as duplicate of #11927. Added diagnostic evidence from this reproduction as a comment there.

github-actions[bot] · 8 months ago

This issue has been automatically locked since it was closed and has not had any activity for 7 days. If you're experiencing a similar issue, please file a new issue and reference this one if it's relevant.

MCP server env vars from .mcp.json not passed to spawned process

Description

Steps to Reproduce

Expected Behavior

Actual Behavior

Diagnostic Evidence

Impact

Environment

5 Comments

Additional Finding: User-scope config also affected

Workaround Found

Related Claude Code issues

Browse by topic