MCP server not loading .env file from extension directory

[shivapoudel]

Pre-reqs

• I've searched the current open issues
• I've updated to the latest versions

Extension Version

0.1.4

Gemini CLI Version

0.26.0

Environment

Darwin Shivas-MacBook-Pro.local 25.2.0 Darwin Kernel Version 25.2.0: Tue Nov 18 21:09:45 PST 2025; root:xnu-12377.61.12~1/RELEASE_ARM64_T6030 arm64

Current Behavior

Although settings says its loaded from .env it is not loading. See screenshot:

If I export variables in .zshrc then it works

export MYSQL_HOST="localhost"
export MYSQL_PORT=10024
export MYSQL_USER=root
export MYSQL_PASSWORD=xxxx
export MYSQL_DATABASE=local

Expected Behavior

Load from .env although configuration saves data.

Steps to reproduce?

1. Install MySQL MCP
2. Configure it
3. Load from variable is missing data from .env
   ...

Additional Details

No response

[shivapoudel]

@averikitsch Can we also include support for socket file for connecting?

[averikitsch]

Thank you @shivapoudel for the issue. Please try upgrading to Gemini CLI version 0.27.0.

[averikitsch]

[@averikitsch](https://github.com/averikitsch) Can we also include support for socket file for connecting?

Thank you for the feature request. Could you make a new GitHub Issue for this feature request?

[shivapoudel]

@averikitsch Still an issue for me to load env variables on Gemini version 0.27.0.

➜  public git:(fix/chromeless-median-flow) gemini extensions list
Loaded cached credentials.
✓ mysql (0.1.4)
 ID: 8a224ff7bdc65f3037d887c266609e2e03533f8b2edaec9af7d3cd8c0f1d5169
 name: 430005175c4c7810996d3481f0dbc3ec01103d6abcc5beec5db4b3f1eae35047
 Path: /Users/shivapoudel/.gemini/extensions/mysql
 Source: https://github.com/gemini-cli-extensions/mysql (Type: github-release)
 Release tag: 0.1.4
 Enabled (User): true
 Enabled (Workspace): true
 Context files:
  /Users/shivapoudel/.gemini/extensions/mysql/MYSQL.md
 MCP servers:
  mysql
 Settings:
  Host: 127.0.0.1 (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  Port: 10024 (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  Database: local (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  User: root (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  Password: *** (User - Keychain)
➜  public git:(fix/chromeless-median-flow) /Users/shivapoudel/.gemini/extensions/mysql/toolbox --prebuilt mysql --stdio
2026-02-05T02:19:08.090799+05:45 INFO "Using prebuilt tool configurations for: mysql" 
2026-02-05T02:19:08.090978+05:45 ERROR "unable to parse prebuilt tool configuration for 'mysql': error parsing environment variables: environment variable not found: \"MYSQL_PASSWORD\"" 

[averikitsch]

I apologize for the issue. We have reported this to the Gemini CLI team and will roll out a fix this week. Thanks!

[averikitsch]

Hi @shivapoudel this is fixed in Gemini CLI v0.28.2.

[shivapoudel]

@averikitsch I have set up using gemini extensions config mysql, and it created all the information in the .env file, and I am on Gemini CLI v0.28.2.

In the .env file, there is no MYSQL_PASSWORD as it's fetched from the Gemini keychain access. While running the command below, it seems it's not fetching.

➜  ~ gemini extensions list
Loaded cached credentials.
✓ mysql (0.1.4)
 ID: 8a224ff7bdc65f3037d887c266609e2e03533f8b2edaec9af7d3cd8c0f1d5169
 name: 430005175c4c7810996d3481f0dbc3ec01103d6abcc5beec5db4b3f1eae35047
 Path: /Users/shivapoudel/.gemini/extensions/mysql
 Source: https://github.com/gemini-cli-extensions/mysql (Type: github-release)
 Release tag: 0.1.4
 Enabled (User): true
 Enabled (Workspace): true
 Context files:
  /Users/shivapoudel/.gemini/extensions/mysql/MYSQL.md
 MCP servers:
  mysql
 Settings:
  Host: 127.0.0.1 (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  Port: 10024 (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  Database: local (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  User: root (User - /Users/shivapoudel/.gemini/extensions/mysql/.env)
  Password: *** (User - Keychain)
➜  ~ /Users/shivapoudel/.gemini/extensions/mysql/toolbox --prebuilt mysql --stdio
2026-02-13T23:28:40.32616+05:45 INFO "Using prebuilt tool configurations for: mysql" 
2026-02-13T23:28:40.326204+05:45 ERROR "unable to parse prebuilt tool configuration for 'mysql': error parsing environment variables: environment variable not found: \"MYSQL_PASSWORD\"" 
➜  ~ 

[averikitsch]

Hi @shivapoudel, you won't be able to run Toolbox directly using ~ /Users/shivapoudel/.gemini/extensions/mysql/toolbox --prebuilt mysql --stdio since the extension saves the value in the keychain. Can you run gemini --debug and see if you are getting the same error?

[shivapoudel]

@averikitsch This is the error I am seeing, although I tried addingthe password in Keychain as well as on the .env file.

But strangely, if the current directory where I am running Gemini has .env file like this then it works.

MYSQL_HOST=localhost
MYSQL_HOST=3306
MYSQL_DATABASE=wordpress
MYSQL_USER=root
MYSQL_PASSWORD=Password@123

Keys findings:

1. If MYSQL_PASSWORD is not set on project .env, it returns error. This should be supported from Keychain.
2. Global .env file variables are correct but still throwing above attachments issue.
3. If we have installed Gemini using Homebrew then after install extension and entering all the promts it says Keychain is not available.

Additionally, can't use dynamic value for .env within project directory like this.

# Database variables.
WORDPRESS_DB_HOST='localhost'
WORDPRESS_DB_NAME='wordpress'
WORDPRESS_DB_USER='root'
WORDPRESS_DB_PASSWORD='Password@123'

# Gemini MySQL MCP variables.
MYSQL_HOST="${WORDPRESS_DB_HOST}"
MYSQL_DATABASE="${WORDPRESS_DB_NAME}"
MYSQL_USER="${WORDPRESS_DB_USER}"
MYSQL_PASSWORD="${WORDPRESS_DB_PASSWORD}"