Whether one reads Cortés' letters or Díaz del Castillo's account, the Spaniards appear to have been deeply religious. In many respects, Spain was one of the most Catholic countries of Europe, in part because of the country's century long struggle to rid itself of its Islamic conquerors and the Spaniards' fierce defense of the "true" religion against both Muslims and Jews. Cortés was forever thanking God for his victories and saw God's will as the source of his success.

It is also apparent from the documents that the Spaniards were appalled by the fact that the native population practiced human sacrifice and ate human flesh. Though the Tlaxcalans later argued that they had accepted Christianity the minute they agreed to ally with the Spaniards that is only partially true. When Xicotencatl agreed to an alliance with Cortés, he gave him two of his daughters, who were baptized and given Christian names. But, while the Tlaxcalans agreed to clean a newly constructed temple so the Spaniards could turn it into a church, they refused to destroy their idols or stop practicing human sacrifice, for they believed that both benefited them.

One figure, Father de la Merced, understood the problem and urged Cortés not to try to impose Catholicism on the Tlaxcalans by force, that it would take time for them to understand and accept Christianity.

After the massacre of the Cholulans, Cortés again demanded that they clean a temple for use as a church, where they could place a cross and an image of the Virgin Mary. Like the Tlaxcalans, the Cholulans agreed to allow the Spaniards to use the temple as a church. But, while promising Cortés that they would destroy their idols, as that was a condition of the peace, they refused to do so. Father de la Merced again stepped in to persuade Cortés not to try to force the Cholulans to convert, as it would take time for them to understand why Christianity was superior.

Religion also became a major issue in Tenochtitlan, where Cortés demanded to enter the interior of the great temple to Huitzilipochtli. Moctezuma at first refused, and then agreed to allow him to climb to its sanctuary at the top with his interpreters, which must have included Malinche, since she was the only one who could understand Nahuatl and Spanish. Since women were not allowed in this sacred space, her presence alone was a violation. Cortés, as usual, demanded to put an image of the Virgin Mary and a cross in the temple, but an incensed Moctezuma refused. After Cortés put Moctezuma under house arrest, this became a major issue for the Spaniards, who finally persuaded Cortés into tricking Moctezuma into allowing him to put the image and the cross in the temple.

One explanation for the attack on those celebrating the festival of Tóxcatl is that the Spaniards believed that the Mexicas were planning a rebellion because of their religious differences and their resentment about the image and the cross in the temple.

Before the Spaniards escaped Tenochtitlan, they climbed the steps of the temple to see if the image and the cross were still there. Díaz del Castillo claims they were not, that Moctezuma had rescued them, but is more likely that the Mexicas destroyed them. Before they left, the Spaniards set fire to the temple.