He studied philosophy and theology in the University of Alcalá. His inclination was first towards the Carthusians because of their life of contemplation, but finally he entered the Society of Jesus at Alcalá in 1555, fifteen years after its foundation. In the novitiate of Simancas he met St. Francis Borgia and a strong affection was established between them. He resumed his philosophical and theological studies at Alcalá and Ávila, under the guidance of the Dominicans, for as yet in Spain the Society of Jesus had no College for theological studies of its own.
The continual interruptions of his studies impeded his progress in scholastic theology, but did advance in the field of mystical theology. He became confessor, master of novices, rector, provincial, and visitor. He was ordained a priest in 1558, and, although only twenty-five years of age, was entrusted with the spiritual direction of St. Teresa, then belonging to the mitigated order of Carmel, but who was on the point of founding the Discalced Carmelites. Alvarez not only guided her in matters of the spirit, but defended her from her critics, encouraged her in her work of reform, and had much to do with framing the rules of the new Order.
Alvarez's direction of Teresa continued for seven years, and it was revealed to her there was no one in the world who surpassed him in sanctity.  He followed the usual method of prayer for sixteen years. In 1574 he was made rector of Salamanca and visitor of the Province of Aragon and, in 1579, was about to be sent as provincial to Peru but that project was never carried out. He was well on in life when his method of prayer was questioned. By some it was looked upon as a delusion of the devil. Alvarez was compelled to write an account of it to the General of the Society of Jesus, Everard Mercurian, who approved of it, but discountenanced it as a general practice. At the same time, he expressed his esteem for Alvarez and employed him in the most responsible offices. At his death, St. Teresa had a revelation of his glory in heaven. He died at Belmonte in 1580.
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