When upgrading MySQL Server on Windows, mysql_upgrade is a crucial command-line utility that performs essential maintenance tasks:

• Checks tables for incompatibilities with the new version
• Repairs tables if necessary
• Updates system tables to the current MySQL structure
• Creates new system tables if they don't exist

The key misconception is trying to run mysql_upgrade from within the MySQL client. It's actually a standalone executable that needs to be run from Windows Command Prompt:

# Navigate to MySQL bin directory (adjust path as needed)
cd C:\\Program Files\\MySQL\\MySQL Server 8.0\\bin

# Execute with proper credentials
mysql_upgrade -u root -p

Error 1064: This occurs precisely because users attempt to run it as SQL command. Remember: mysql_upgrade is an external program, not SQL syntax.

Permission Problems: Run Command Prompt as Administrator when executing:

mysql_upgrade --force -u root -p --upgrade-system-tables

After successful execution, check the output for any warnings. You can verify system table updates with:

mysql -u root -p -e "SELECT * FROM mysql.user LIMIT 1;"

For deployment scenarios, include this in your post-installation scripts:

@echo off
set MYSQL_PATH="C:\\Program Files\\MySQL\\MySQL Server 8.0\\bin"
cd %MYSQL_PATH%
mysql_upgrade -u admin -pP@ssw0rd --silent

• Always backup databases before running mysql_upgrade
• The server must be running during execution
• Consider using --force flag if encountering minor errors
• For MySQL 8.0+, the utility handles both schema and system table upgrades

Many Windows administrators face confusion when trying to run mysql_upgrade after a fresh MySQL installation or upgrade. The crucial point often missed is that this is a command-line utility, not a SQL command to be executed within the MySQL client.

1. Ensure MySQL service is running (check via Services.msc or net start mysql)
2. Verify your PATH includes MySQL's bin directory (typically C:\Program Files\MySQL\MySQL Server X.X\bin)
3. Have administrator privileges for the command prompt

Here's the proper way to execute mysql_upgrade:

:: Open Command Prompt as Administrator
cd "C:\Program Files\MySQL\MySQL Server 8.0\bin"
mysql_upgrade -u root -p

You'll be prompted for your root password. For alternative authentication:

mysql_upgrade --user=root --password=[your_password] --host=localhost

For scripting purposes or repeated upgrades, consider creating a batch file:

@echo off
set MYSQL_PATH="C:\Program Files\MySQL\MySQL Server 8.0\bin"
cd /d %MYSQL_PATH%
mysql_upgrade -u root -p[password] --force
pause

After execution, check the output for:

• "Upgrade process completed successfully" message
• Any tables marked as "OK" or "Upgraded"

Common errors include:

ERROR 1045 (28000): Access denied for user 'root'@'localhost'
:: Solution: Verify credentials or use --skip-grant-tables option

ERROR 2003 (HY000): Can't connect to MySQL server
:: Solution: Ensure MySQL service is running

For complex scenarios:

:: Upgrade specific databases only
mysql_upgrade -u root -p --databases db1 db2

:: Force upgrade even if version matches
mysql_upgrade -u root -p --force

:: Write debug information
mysql_upgrade -u root -p --verbose

Always:

1. Backup your databases before running mysql_upgrade
2. Review the mysql_upgrade_info file created in data directory
3. Consider running ANALYZE TABLE on upgraded tables
4. Restart the MySQL service after upgrade