He received in 1969 his doctorate from the Sorbonne with dissertation L’Économie de l’empire portugais aux XVe et XVIe siècles.
He was a full professor of the Faculty of Social Sciences and Humanities of the Universidade Nova de Lisboa and coordinator of the department of sociology from 1975 to 1988.
He helped to introduce to Portugal a modern version of economic and social history, according to principles enunciated by Henri Berr and Fernand Braudel.
Magalhães Godinho preferred to turn away from a strictly event-driven or biographically-oriented history (such as a biography of the prince Henry the Navigator) to try to draw the social and cultural picture of an era and a milieu.
His supporters believe that he broke with the narrow conservatism and ignorance of the political, economic and social sciences that marked Portuguese historiography before his works.