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The MegaSquirt-I™ EFI Controller uses a flash-based Motorola microprocessor (MC68HC908GP32) for the calculation of fuel pulse width and injector control. Additionally, host software (Windows-based) was developed which allows the run-time adjustment of control parameters.

In 2005, MegaSquirt-II, a replacement daughtercard for the MegaSquirt-I™ EFI Controller's 68HC908 processor became available from Bowling and Grippo. This daughtercard included a much faster processor and increased memory, and also included control options for stepper style IAC controllers and ignition systems. All but the earliest version of MegaSquirt-II are CAN (controller area network) enabled, allowing them to 'talk' to add-on modules such as sequential injections drivers and transmission controllers.