The PMMA offers two (2) major programs, namely: Bachelor of Science in Marine Transportation (BSMT) and Bachelor of Science in Marine Engineering (BSMarE). These programs are four-year residency courses consisting of a three-year academic studies (1st, 2nd and 4th year) and one year apprenticeship training on the 3rd year on board commercial vessels plying the international routes as deck or engine cadets.

The course structures are designed in a manner that the first two years of academic period prepares the midshipmen for sea-phase training giving them the necessary knowledge and skills required on board as cadets. The third year is the sea-phase training. At the end of the training, the midshipmen should have fulfilled the requirements for Regulation II/4 of the STCW Convention (minimum knowledge required for certification of officer-in-charge of a navigational watch on ships of 200 gross register tons or more) and the requirements of Regulation III/4 of the STCW Convention (minimum knowledge required for certification of chief engine officers of ships powered by main propulsion machinery of 3000 kW or more).

The last academic period is the professional stage. It is at this stage where the graduating midshipmen are being equipped with additional knowledge and skills required on them as Third Mates and Fourth Marine Engineers. Likewise, they are also being developed to acquire a sense of responsibility that an officer and a gentleman should possess.

These programs are continuously reviewed, amended, and presently designed in such a way that it would meet the needs and requirements not only that of the Commission on Higher Education and the local maritime industry, but internationally, as well.