To the 6809 specifications, it adds higher clock rates, enhanced features, new instructions, and additional registers.

Most of the new instructions were added to support the additional registers, as well as up to 32-bit math, hardware division, bit manipulations, and block transfers.

FM, a Japanese magazine for Fujitsu personal computer users, contained the first description of the 6309's additional capabilities.

(Several Japanese computers had 63C09 CPUs clocked with a 3.58 MHz colorburst crystal, so the 3.5 rating seems most likely).

Anecdotal and individual reports indicate that the 63C09 variant can be clocked at 5 MHz with no ill effects.

Like the 6809, the Hitachi CPU comes in both internal and external clock versions (HD63B/C09 and HD63B/C09E respectively) When switched into 6309 Native Mode (as opposed to the default 6809-compatible mode) many key instructions will complete in fewer clock cycles.

Genuine 6309 additions include inter-register arithmetic, block transfers, hardware division, and bit-level manipulations.

[citation needed] Careful analysis should be done to ensure that the programmer uses the most efficient code for the particular application.

The illegal instruction fetch is not maskable, and many TRS-80 Color Computer users reported that their 6309's were "buggy" when in reality it was an indicator of enhanced and unknown features.