The general finally relented and allowed José to become the flagbearer of the troop. The Cristeros nicknamed him Tarcisius, after the early Christian saint, martyred for protecting the Eucharist from desecration.
To break his resolve, he was made to watch the hanging of another Cristero that they had in custody, but instead José encouraged the man, saying that they would soon meet again in Heaven. In prison, José prayed the rosary daily and wrote an emotional letter to his mother, saying that he was ready to fulfill the will of God. His father attempted to raise a ransom to save him, but was not able to appease the government in time.
On the evening of February 10, 1928, "they cut the bottom of his feet and obliged him to walk around the town toward the cemetery. They also at times cut him with a machete until he was bleeding from several wounds. He cried and moaned with pain, but he did not give in. At times they stopped him and said, 'If you shout, "Death to Christ the King" we will spare your life.' José would only shout, 'I will never give in. Viva Cristo Rey!'"
When they reached the place of execution, his captors stabbed him numerous times with bayonets. The commander was so furious that he pulled out his pistol and shot José. Moments before his death, the boy drew a cross in the dirt and kissed it.