When John finished his studies, Don Alonso offered him a secure future: ordination to the priesthood and the post of chaplain at the hospital. In turn, the young man could have then assisted his mother and brother out of their poverty, a goal toward which he must have felt the strongest urgings. The Jesuits, who appreciated his intellectual gifts and piety, also made their overtures. But surprisingly, in 1563, at age 21, John entered the Carmelite novitiate recently founded in Medina. What prompted this unexpected decision was probably Carmel's contemplative spirit and its devotion to Mary, the mother of God. Receiving the name Fray (Brother) John of St. Matthias, he passed his novitiate year, we can suppose, studying the Carmelite Rule and the order's ancient spirituality. In The Book of the First Monks, a medieval Carmelite work on the spirit of the order that John must have pondered over during his novitiate, the following teaching stands out:
The goal of this life is twofold. One part we acquire, with the help of divine grace, through our efforts and virtuous works. This is to offer God a pure heart, free from all stain of actual sin. We do this when we are perfect and in Cherith, that is, hidden in that charity of which the Wise Man says: "Charity covers all sins " [Prov. 10:12]. God desired Elijah to advance thus far when he said to him: "Hide yourself by the brook Cherith " [1 Kgs. 17:3-4]. The other part of the goal of this life is granted us as the free gift of God: namely, to taste somewhat in the heart and to experience in the soul, not only after death but even in this mortal life, the intensity of the divine presence and the sweetness of the glory of heaven. This is to drink of the torrent of the love of God. God promised it to Elijah in the words: "You shall drink from the brook. " It is in view of this double end that the monk ought to give himself to the eremitic and prophetic life.
It must have been toward the end of 1564 that John of St. Matthias, after his novitiate year, arrived in Salamanca for studies in philosophy and theology. The sight of the university town with its churches and cathedrals, palaces and lordly estates undoubtedly thrilled him. In its period of greatest splendor, the university of Salamanca boasted professors of high prestige, large numbers of students from all parts of Spain, an emphasis on biblical and theological studies, and a variety of schools of thought. It ranked with the great universities of Bologna, Paris, and Oxford. There you would find Fray Luis de León, who taught theology in the chair of Durando; Mancio de Corpus Christi, a worthy successor of Vitoria and of Melchor Cano, who held the chair of Prime, the most important in the university; the Augustinian Juan de Guevara, who gave the afternoon lecture and whose explanations were called miraculous; Gregorio Gallo, in place of Domingo Soto, who took over the chair of Sacred Scripture; and Cristóbal Vela, who gave lectures on Scotus. John's name appears on the matriculation records in the school of arts for three years. Knowledge has reached us about the courses that were offered there and the names of the eminent men who held professorships. Master Enrique Hernández, the author of a treatise on philosophy, taught the classes in natural philosophy; Francisco Navarro held the chair of ethics; Hernando Aguilera, who had worked out an astrolabe, reigned in the chair of astronomy; Francisco Sanchez taught grammar and even today is considered an authority on this subject; Master Martin de Peralta explained the Summulas (an introduction to logic); and Juan de Ubredo held the chair of music. The statutes of the university prescribed the works of Aristotle for the arts course, but this merely meant that a text from the Philosopher was to be read at the beginning of the lecture; the professor could then go on to interpret it with full liberty, if not leave it aside entirely. It is not known, though, which classes John actually followed in the arts course.
In the school year 1567-68, John registered in theology. Again, no record tells of the courses he took. He would probably have assisted at the Prime lecture, which went on for an hour and a half, beginning early in the morning. At this lecture, the Dominican Mancio de Corpus Christi explained the Summa theologiae of St. Thomas Aquinas. He followed the method and style of the Dominican school initiated by Vitoria and Cano. It comprised a return to the sources (Sacred Scripture, the Fathers of the Church, and Aquinas) along with a concern for dealing with new themes and contemporary questions. This theology was expressed in sober and direct language. Whether John might have attended Gaspar Grajal's lectures in Sacred Scripture is a matter for speculation. At the time there was a lively struggle within the university over the interpretation of Scripture. The "scholastics, " tenacious partisans of fidelity to the biblical tradition of the preceding centuries, opposed the "scripturists, " who sought the literal sense of Scripture through development of scientific methods and the study of languages. Grajal was prominent among the "scripturists " and later, because of his ideas, was sent to prison for a time by the Inquisition. Besides studies at the university, the Carmelite students, like all religious, had to study at home the doctors belonging to their own order, especially John Baconthorp (c. 1290-1348) - a grandnephew of Roger Bacon - who had taught at the University of Cambridge.
We are told that Fray John was remarkable for his "outstanding talent " and application, testimony bolstered by his appointment as prefect of studies while still a student. With this office went the obligation to teach class daily, defend public theses, and resolve objections that were raised. But for some reason the brilliant young Carmelite was dissatisfied. Was it with the academic atmosphere where the pursuit of knowledge too easily turned into a pursuit of self-exaltation, a quest for titles, chairs, promotions, and awards? Was John beginning to discern there a stubborn attachment to familiar systems of thought, and a reluctance to admit the ultimate inadequacy of all speculations? Was this what he had sought in making his vows? In any case, his horizons lay elsewhere; he found his attention turning frequently to the purely contemplative Carthusians. Though John enjoyed his studies, the contemplative life that had originally attracted him to Carmel was now struggling for first place.