From Imperial Spain: 1469-1716, by J. H. Elliott (Penguin, 2002), 2nd ed., Kindle Loc. 1782-1806:
Isabella‘s faith was fervent, mystical, and intense, and she viewed the present state of the Church with grave concern. It suffered in Spain from the abuses commonly ascribed to it throughout fifteenth-century Europe: pluralism, absenteeism, and low standards of morality and learning in secular and regular clergy alike. Concubinage in particular was accepted as a matter of course, and was no doubt further encouraged by a practice apparently unique to Castile, whereby the child of a cleric could inherit if his father died intestate. In some sections of the Church, however, and especially in the Religious Orders, there was a deep current of discontent at the prevailing laxity; in particular, the Queen’s Jeronymite confessor, Hernando de Talavera, constantly urged upon her the need for total reform. Under Talavera’s guidance, the Queen devoted herself wholeheartedly to the work of raising the moral and intellectual standards of her clergy. As effective nomination to bishoprics came to be increasingly exercised by the Crown, the morals and learning of candidates ceased to be regarded as largely irrelevant details, and high social rank was no longer an essential passport to a diocese. As a result, the standard of the Spanish episcopate rose markedly under the Catholic Kings, although some of Ferdinand’s own appointments still left a good deal to be desired. Cardinal González de Mendoza, who succeeded Carrillo at Toledo in 1482, hardly conformed to the model of the new-style prelate; but the remarkable munificence of his patronage no doubt did something to atone for the notorious failings of his private life. In 1484 he founded at Valladolid the College of Santa Cruz, which set the pattern for further foundations designed to raise educational standards and produce a more cultivated clergy; and he probably did more than any other man to foster the spread of the New Learning in Castile.
While the Queen and her advisers worked hard to raise the standards of the episcopate and the secular clergy, a movement was gaining ground for reform of the Religious Orders. The Franciscan Order had long been divided between Conventuales and Observants, who wanted a return to the strict simplicity of the Rule of St. Francis. Among the Observants was the austere figure of Francisco Jiménez de Cisneros, whom the Queen regarded as a providential substitute for her confessor Talavera, when the latter became first Archbishop of Granada in 1492. Already in 1491 Alexander VI had authorized the Catholic Kings to take in hand the reform of the monastic orders, and two years later Cisneros launched himself with characteristic energy into the work of reform, and continued to direct it with unflagging vigour after his appointment to Cardinal Mendoza’s see of Toledo on the cardinal’s death in 1495. Starting with his own Order, the Franciscans, he set about imposing a strict observance of the Rule in face of the most intense opposition. The Franciscans of Toledo, expelled from their convent, came out in procession beneath a raised cross, intoning the Psalm In exitu Israel Aegypto, while four hundred Andalusian friars preferred conversion to Islam and the delights of domesticity in North Africa to a Christianity which now suddenly demanded that they adandon their female companions. Slowly, however, the reform advanced. It spread to the Dominicans, the Benedictines, and the Jeronymites, and by the time of Cisneros’s death in 1517 not a single Franciscan ‘conventual’ house remained in Spain.