At the age of eighteen Molina became a member of the Society of Jesus. He studied theology at Coimbra. After this, he became professor in the university of Évora, Portugal. From this post he was called, at the end of twenty years, to the chair of moral theology in Madrid.
Besides other works he wrote De liberi arbitrii cum gratiae donis, divina praescientia, praedestinatione et reprobatione concordia (4 vo., Lisbon, 1588); a commentary on the first part of the Summa Theologiae of Thomas Aquinas (2 vols., fol., Cuenca, 1593); and a treatise De jure et justitia (6 vols., 1593-1609).
De Hispanorum primogeniorum origine ac natura, 1588
De iustitia et iure, 1733