The MAP-i structure consists of a first curricular year (starting in the fall and divided into two semesters) featuring three mandatory courses in foundations of computing, programming paradigms and information technologies. Each course corresponds to 42 lecturing hours and lasts one complete semester. Beyond the mandatory courses, the students are offered a number of optional courses taught by professors from MAP universities and leading scientists from abroad. The graduate students are expected to take some credits in matters not directly related to their field of study. Also included is a graduate seminar with lectures by international experts and working visits to MAP associated research centers and laboratories.

In the first semester, the student must choose his topic of dissertation from a list of possible research projects. Based on this choice, the student must prepare during the second semester his thesis proposal, which includes an extensive review of the state of the art, a set of detailed objectives and methods, outline of potential contributions and a roadmap to achieve them. The thesis proposal should be delivered up to 18 months after starting the program.

Following this curricular year, which is worth 60 credits in the European Credit Transfer System (ECTS), and which includes the elaboration of a thesis proposal (15 ECTS), the graduate student enters the research and thesis development phase, which lasts for 2 to 3 years and corresponds to at least 120 ECTS.

In terms of organization, the MAP universities agreed upon a general model, in which the curricular part is taught entirely in one of the institutions, rotating every year between Minho, Aveiro and Porto. Each student receives individual guidance by a mentor, who suggests a supervisor and possibly a co-supervisor. Beyond the regular thesis supervision, the student's progress will be monitored by a PhD committee consisting of two other recognized experts in the field, one of which from an outside institution. Submission of the thesis and thesis defense follow standard international practice. A student will be awarded a doctorate, in the form of a joint PhD degree by the Universites of Minho, Aveiro and Porto, if his thesis is judged to represent an original contribution to knowledge in the chosen area.