As the emulator progressed, support was added for FreeBSD, AROS, and OS X, but these ports were not maintained as much or as well as the Linux and Windows versions.

Over time, the emulator expanded, maintained and improved extant video plug-ins, and provided extra features beyond the project's original scope.

Like many N64 emulators (including Sixtyforce, 1964, and Project64), Mupen64Plus uses four modular plug-ins (dynamic libraries) which adhere to a specification written by Project64 developer Zilmar.

For this reason, the Mupen64Plus team presented a design proposal to modify the plugin application programming interface (API) to place all of the user interface code in one software module and make other improvements to streamline the operation of a cross-platform N64 emulator.

Brandon Widdler of Digital Trends considers the emulator one of the best for the Nintendo 64 along with Project64, citing its cheat functions, dynamic recompilers for 32-bit and 64-bit machines, and speed adjustment feature.