In June of 1577, Ornaneto, the Nuncio who had been so friendly toward the Discalced, died. His death, together with the disturbing news that the Discalced had convened the Chapter at Almodovar, prompted the Calced to executed the resolutions of Piacenza. Thus during the night of December 2, 1577 a group of Calced Fathers, men-at-arms, and some seculars, seized Fray Juan and his companion to bring them to a Calced monastery. Fray John of the Cross was taken to Toledo where the acts of the Chapter of Piacenza were read to him and a complete renunciation of the Reform was demanded. If he refused to renounce the Reform, he would be declared a rebel. But Fray John of the Cross did not renounce it. He was keen-minded enough to distinguish properly in this maze of conflicting jurisdiction and conclude that the proscriptions of the Chapter were directed against the friars of Granada, Seville, and Penuela, and not against him, and that he had been at his post at the Incarnation by the orders of the Nuncio, which were still in effect. However, the tribunal called him both rebellious and contumacious and prescribed imprisonment.
Fray John was led to his prison cell, a little room originally intended as a closet, six feet wide and ten feet long. It had no window; the only opening was a slit high up in the wall. It was frightfully cold there in winter, and suffocating in summer. They deprived him of his hood and scapular as a token of punishment for his rebellion. His food was bread, sardines, and water. Three evenings a week he had to eat kneeling on the floor in the middle of the refectory. Then when the friars were finished their supper, his shoulders were bared and each member of the community struck him with a lash, some very vigorously, for the wounds he received world not heal properly for years. This scourging lasted for the time it takes to recite the Psalm Miserere. Since he continued in his refusal to renounce the Reform, they would then conduct him back to his bleak prison. No compassion could be shown him, for the Constitutions under the most severe penalties forbade one to show favor to a prisoner. After six months of prison life, the Saint was assigned a new warder. This one did manifest some elements of compassion; for instance, he gave him a change of clothes, and also furnished him with paper and ink, thus enabling him in these sad surroundings to write down the great lyric poems which, as a means of passing the time, he had been composing in his mind.
Taking advantage of the leniency of his new jailer, Fray John familiarized himself with every aspect of the monastery during his daily reprieves from the prison cell. On the night of August 16, 1578, in a manner some declare was miraculous, he managed to escape and find his way to the Discalced nuns in Toledo, who hid him from the search party. Eventually he was able to journey to El Calvario in the south of Spain, where he was safer and had the opportunity to restore his health.