Fray Pedro had developed a fatherly knowledge of, and love for, the Guale. Even so, he knew there are certain truths that cannot be ignored and out of both duty and love, Fray Pedro admonished the young Guale prince, Juanillo, for his polygamy (that is, having more than one wife). Governor Menéndez and the Franciscan Friars trusted and respected Juanillo’s father, the chief of the Guale, so, consequently, they also trusted his son and heir, Juanillo.

But Juanillo was outraged at Fray Pedro’s gentle reproof, and thus, the rebellion of the Guale began with the martyrdom of Fray Pedro. The Guale, led by Juanillo, killed Fray Pedro in the early morning of September 14th, 1597 as he was preparing to offer Mass on the Feast of the Exaltation of the Holy Cross. He had just finished praying Lauds and was about to walk over to the chapel. Accounts of the time indicate that the young men snuck up on him and clubbed him to death, chopping off his head, and shamefully displaying it upon a spike. Juanillo would go on to set off a chain of martyrdoms throughout the Franciscan missions.