He was a professor of theology at the Jesuit-run Ateneo de Manila University from 1965 to 1988. In the context of the Filipinization movement and radicalism in the university, provoked in part by the declaration of martial law in 1972, Bonoan advanced a Filipino theology without relying on Western paradigms. His course in theology was unique in its focus on history and the local context in which Christianity had developed. During this time, Bonoan also served as moderator of the Ateneo Catechetical Instruction League (ACIL), acted as spiritual adviser to students, and led community efforts to aid flood victims of Central Luzon.
