His work on logic and metaphysics made him known in his time as the Portuguese Aristotle; he projected the 'Cursus Conimbricensis' realized by Manuel de Góis and others.

Pedro da Fonseca was born in Proença-a-Nova, Portugal, in 1528 and joined the Society of Jesus in Coimbra in 1548.

In logic, where his thinking was more closely aligned with humanism than with scholasticism, his main publications were Institutionum Dialecticarum (1564), and Isagoge Philosophica (1591).

But his greatest claim to lasting reputation lies in the fact that he first devised the solution, by his scientia media in God, of the perplexing problem of the reconciliation of grace and free will.

Nevertheless his fame in this matter has been somewhat obscured by that of his disciple, Luis de Molina, who, having more fully developed and perfected the ideas of his master in his work Concordia Liberi Arbitrii cum Gratiæ Donis, came gradually to be regarded as the originator of the doctrine.