In June 1588, he was elected third Councillor to the Vicar General for the Discalced Carmelites, Father Nicolas Doria. To fulfill this role, he had to return to Segovia in Castile, where he also took on the role of prior of the monastery. After disagreeing in 1590–1 with some of Doria's remodelling of the leadership of the Discalced Carmelite Order, John was removed from his post in Segovia, and sent by Doria in June 1591 to an isolated monastery in Andalusia called La Peñuela. There he fell ill, and travelled to the monastery at Úbeda for treatment. His condition worsened, however, and he died there, of erysipelas on 14 December 1591.