After the demise of Commodore, the later owners of the Amiga trademark granted a license to a German company called Haage & Partner to update the Amiga's operating system. Along with this update came a change in the way people referred to the Amiga's operating system. Rather than specifying "Kickstart" or "Workbench", the updates were most often referred to as simply "AmigaOS". Whereas all previous OS releases were Motorola 68000 compatible, some OS components from release 3.5 onwards required a 68020 or better.

Updates included:
CD filesystem support as standard
Distribution on CD instead of floppy disk
Supplied with TCP/IP stack (unregistered time limited freely MiamiDX demo in 3.5, unlicenced, unrestricted AmiTCP/IP in 3.9), web browser (AWeb), and e-mail client
Improved GUI, called "ReAction"
AVI/MPEG movie player (OS3.9)
Support for hard disks larger than 4GB (a limitation from 1.x)
HTML documentation (English and German)
MP3 and CD audio player (OS3.9)
Dock program (OS3.9)
Improved Workbench
Find utility (OS3.9)
ASync workbench (no more waiting for files to be copied)
Unarchiving system called XAD (OS3.9)
Support for PowerPC CPUs through Haage & Partner's multi-tasking kernel "WarpOS" which operated alongside AmigaOS
Limited OS support for PowerPC CPUs, for example in picture.datatype (OS3.9)