At Trent he came into connection with Cardinal Petrus Pacheco, Bishop of Jaen (consequently called "Giennensis"), who was a patron of the Franciscan Order.
Vega was conspicuous in the preliminary discussions of the canon of the Scriptures and on the Vulgate, which were treated in the Decree promulgated in the fourth session of the council, 8 April 1546.
Previous to the council Vega had written to defend the Catholic doctrine of justification against the Protestants, "De justificatione, gratia fide, operibus et meritis quaestiones quindecim" (Venice, 1546).
After the promulgation of the Decree he wrote in its defence at Trent and Venice, "Tridentini decreti de justificatione exposition et defensio lib.
Peter Canisius had it reprinted at Cologne (1572) in one volume with Vega's previous work, "De justificatione".