After joining the Society of Jesus, Fonseca studied philosophy at Sanfins and Évora, eventually receiving his doctorate in theology from the University of Évora in 1570. Fonseca taught philosophy at the Colegio das Artes at Coimbra, where he earned the moniker “the Portuguese Aristotle.” He claims to have invented the doctrine of Middle Knowledge while lecturing on divine providence at Coimbra in 1566 (In Metaph. III.6.2.4.8). It is probably no coincidence that the famous advocate of Middle Knowledge, Luis de Molina, was a student at Coimbra that year. Fonseca also occupied several ecclesiastical administrative positions (Tavares 1953). As provincial of Portugal he commissioned Emmanuel Goës to publish the famous Comentarii Collegii Coninmbricensis (Backer, 2:1273) (see Conimbricenses). While on administrative assignment in Rome, he contributed to the redaction of the Ratio Studiorum (see Jesuit).

Descartes may have been familiar with Fonseca's popular logic textbook, Institutionum Dialecticarum Libri Octo, as well as Fonseca's introduction to Aristotle's Categories, Isagoge Philosophica. These works were printed together at La Flèche in 1609, and the former is recommended by name in the Ratio Studiorum. Fonseca also wrote commentaries on Aristotle's Metaphysics, but it is hard to say whether Descartes read them.

Fonseca held many of the Aristotelian views against which Descartes reacted, such as a hylomorphic conception of substance and the Aristotelian view that “nothing is apprehended by the intellect that was not first cognized somehow by the senses” (In Metaph. V.2.1–2, I.1.4.3) (Des Chene 1996; Secada 2000, 11–16) (see form, substantial). Fonseca also held versions of the Scholastic doctrines later adopted by Descartes, such as the distinction between formal and objective concepts, which prefigures Descartes’ distinction between formal and objective reality, and a version of the modal distinction that would later reach Descartes, in a modified form, by way of Suárez (In Metaph. IV.2.2.1, V.6.6.2) (see being, formal versus objective).