John must have felt consolation and peace when a year and a few months previous to this he arrived to take up his office at El Calvario, a place of spectacular beauty far away from the jurisdictional conflicts and threats. He never cared to go over the past and talk about his imprisonment. He bore no animosity; he neither complained nor boasted about what he had endured. Now more than ever he could listen to nature through his senses; the flowers, the whistling breezes, the night, the dawn, the rushing streams, all spoke to him. God was present everywhere.
But in less than a year he had to move to the city again, this time to the university town of Baeza to serve as rector of the new college for the Teresian friars in the south. Unable to compete with places like Salamanca or AlcalΓ‘, the univesrsity of Baeza did enjoy a certain prestige and was making important contributions to Scripture studies. While rector of the Carmelite college (1579-82), John guided his own students in their studies, becoming acquainted as well with the professors at the university. Records reveal that they frequently consulted and had long conversations with him about the Bible. In these years after his escape, John took up once more the ministry of spiritual direction, not only of the friars but also of the nuns. He made frequent journeys through the mountains to Beas, a typical little Andalusian town with small whitewashed houses, grilles in front of large windows, and balconies full of flowering plants. The town is important in John's life, for here he met Ana de JesΓΊs, the prioress, who did not at first recognize his depth and spirituality. In a letter to Ana, responding to her complaint about having no spiritual director, Teresa made clear her thoughts about Fray John of the Cross:
I'm really surprised, daughter, at your complaining so unreasonably, when you have Father Fray John of the Cross with you, who is a divine, heavenly man. I can tell you, daughter, that since he went away I have found no one like him in all Castile, nor anyone who inspires people with so much fervor on the way to heaven. You would not believe how lonely his absence makes me feel. You should reflect that you have a great treasure in that holy man, and all those in the monastery should see him and open their souls to him, when they will see what great good they get and will find themselves to have made great progress in spirituality and perfection, for our Lord has given him a special grace for this [December 1578].
She went on to extol his holiness, kindness, experience, and learning. Soon Ana de JesΓΊs and her nuns affirmed Teresa's words through their own experience. John shared his poems with them, and began the work of commentary through his talks to them on his Spiritual Canticle. While the saintly friar served as rector at Baeza, his discalced brethren, through the intervention of the king, obtained juridical independence. In 1580 the Holy See allowed them to erect an autonomous province, but under the higher jurisdiction of the general of the order. Complete independence did not come until 1593, after the deaths of both Teresa and John, when Pope Clement VIII accorded the discalced Carmelites the same rights and privileges as other religious orders. In 1582, Fray John was elected prior of a monastery adjacent to the site of the Alhambra, with an outstanding view of the Sierra Nevada and overlooking the enchanting city of Granada with its exotic traces of Moorish culture in evidence everywhere. Here, in addition to leading the community, John designed and worked on a new aqueduct and a new monastery building that became a model for the discalced. At the same time, his ministry of spiritual direction - not only to the friars and nuns but also to the clergy and lay people who came knocking at the monastery door seeking help - set in motion his work as a writer, and he began to compose his classic works of spirituality. In 1585, at a chapter in Lisbon, John was elected vicar provincial of Andalusia. This office obliged him to travel frequently. He had to attend all the houses of friars and nuns in Andalusia, visiting each formally at least once a year. He founded seven new monasteries. All this brought him to CΓ³rdoba, MΓ‘laga, Caravaca, JaΓ©n, and other renowned cities in the south of Spain.