MST initially offered a four-year non-degree theology program for candidates to the priesthood. In 1977, the Philippine government approved its Graduate School Program and mandated the conferral of the academic degree of Master of Arts in Theology.

An increase in the enrollment of lay and non-clerical religious students motivated the administration to develop further its curriculum. This led to the creation of two tracks in the graduate program: the General Theology Program (GTP) and the Adult Theological Education Program (ATEP)

The General Theology Program (GTP)
Primarily designed for seminarians, religious, and even laypersons studying full-time in Maryhill. The school offers two master's degrees to students attending this track:

                Master of Arts in Theological Studies (MATS)

                Master in Pastoral Ministry (MPM)

The Adult Theological Education Program (ATEP)
Offers on-going theological formation to priests, religious, and laypersons who take courses in the program for either personal updating or for credits leading to a master's degree. MST offers two such degrees to students in this track:

                Master of Arts in Religious Studies (MARS)

                Master of Arts, major in Pastoral Ministry (MAPM)