The MEGA STE is based on STE hardware. This offers better ST compatibility than the TT, and contains several TT functions; the ST-grey version of the TT case with a separate keyboard and system unit, optional FPU, two extra RS232 ports (all 9-pin rather than 25-pin as previous models had), a LocalTalk/RS-422 port, a 1.44 MB HD floppy support, as well as for a third or middle mouse button. In contrast with the 1 MB model, the 2 MB and 4 MB models both feature an internal SCSI harddisk and came with a high resolution monochrome monitor.

The MEGA STE also features a VMEbus expansion slot. The VMEbus allows the system’s capabilities to be enhanced through expansion cards. These expansions include, for example, improved graphics capabilities or ethernet connectivity.

Compared to earlier Atari systems, a special characteristic of the MEGA STE is the software-switchable CPU speed. The CPU can run at 16 MHz to improve processing speed, or at 8 MHz for better compatibility with older software. After the first units were shipped, an upgrade was developed that upgraded the onboard ROMs to TOS 2.05, and later to 2.6/2.06.