Book:OTRS 3.0 - Admin Manual/Chapter 3/4

There's currently no in-place upgrade available for OTRS installations that were done with the Windows Installer. The upgrade process basically consists of backing up the database and the filesystem, uninstalling OTRS, installing the new version, restoring the database and running the upgrade procedure if needed.

Upgrading is described in FAQ# 4200351, and there is also an informative YouTube video available.