How to fix ERROR 1558 (HY000): Column count of mysql table wrong in MySQL

First, gracefully shut down the MySQL service to prevent any data corruption:

# On systemd systems (Linux)
sudo systemctl stop mysql

# Or on traditional systems
sudo service mysql stop

# On macOS with Homebrew
brew services stop [email protected]

# Or manually kill the process
sudo mysqladmin shutdown

Wait a few seconds to ensure the process has fully stopped before proceeding.

The mysql_upgrade utility updates MySQL system tables to match your current MySQL version. This is the primary fix for ERROR 1558:

# Standard invocation (prompts for password)
mysql_upgrade -u root -p

# Non-interactive if you have .my.cnf configured
mysql_upgrade -u root -p --password=your_password

# Force the upgrade even if tables seem compatible
mysql_upgrade -u root -p --force

The utility will:
- Check all tables in all databases for compatibility
- Upgrade system tables to the current version
- Rebuild the privilege tables with new columns
- Clear deprecated columns and settings

After mysql_upgrade completes successfully, restart the MySQL service:

# On systemd systems
sudo systemctl start mysql

# Or on traditional systems
sudo service mysql start

# On macOS
brew services start [email protected]

The server should start without errors. If you still see ERROR 1558, there may be additional corruption.

Test that MySQL is working properly and the error is resolved:

# Connect to MySQL
mysql -u root -p

# At the MySQL prompt, run:
SELECT VERSION();
SELECT COUNT(*) FROM mysql.user;
SHOW TABLES FROM mysql;

If these commands execute successfully without ERROR 1558, the issue is fixed. Your databases and data remain intact.

If you're using MariaDB instead of MySQL, use the MariaDB-specific upgrade command:

# Stop MariaDB
sudo systemctl stop mariadb

# Run MariaDB upgrade utility
mariadb-upgrade -u root -p

# Restart MariaDB
sudo systemctl start mariadb

In newer versions of MariaDB/MySQL, the upgrade is performed automatically on startup if system tables are out of date.