When the Cristero War broke out in 1926, his brothers joined the rebel forces, but his mother would not allow him to take part. The rebel general, Prudencio Mendoza, also refused his enlistment. The boy insisted that he wanted the chance to give his life for Jesus Christ and so come to Heaven easily. 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.

During heavy fighting on 25 January 1928, Mendoza's horse was killed, and José gave his horse to the general so that the fight could go on. Then he sought cover and fired at the enemy until he ran out of ammunition. The government troops captured the boy and imprisoned him in the sacristy of the local church.
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José's killing was witnessed by two childhood friends. It was later reported that José was "captured by government forces", who ordered him to "renounce his faith in Christ, under threat of death. He refused to accept apostasy".

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 after death. 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 to whom he dedicated himself. His father attempted to raise a ransom to save him, but was not able to appease the government in time to do so, thus failing to secure the release of his son.

Others recalled the gruesome events that transpired after the government's failure to break José's resolve on the evening of 10 February 1928: "Consequently 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.