Juanillo left the mission in anger to recruit Natives from the interior to rid the Guale territory of the "troublesome" friars. Under cover of darkness on a Saturday night, the war party crept into the Mission compound and waited for dawn. Fray Pedro was about to leave his cabin to celebrate Mass the next morning, Sunday, September 14, the Feast of the Exaltation of the Holy Cross, when the war party broke in and slew the missionary with a blow of the macana, the Guale version of the tomahawk. With Christian morality thrown aside, a licentious celebration ensued during which Fray Pedro’s severed head was displayed on a pike at the mission landing. The body was left to decay in the sun for several days and then buried in an unmarked grave so that it would never be recovered.
The war party now proceeded to Tupiquí and seized Fray Blas. During the two days he was held prisoner, he was permitted once to celebrate Mass and preach his last sermon. "My sons, for me it is not difficult to die. Even if you do not cause it, the death of this body is inevitable. We must be ready at all times, for we, all of us, have to die someday. But what does pain me is that the Evil One has persuaded you to do this offensive thing against your God and Creator. It is a further source of deep grief to me that you are unmindful of what we missionaries have done for you in teaching you the way to eternal life and happiness." He distributed his personal things among his flock, and then, bound by ropes, watched the profaning of the sacred images, vestments, and vessels. On September 16, he was clubbed to death. After his body was left exposed for several days, a faithful Christian buried it in the woods, where it was found later by a detachment of Spanish infantry sent from St. Augustine to investigate the deaths.
Meanwhile, the war band sent word to the local chief on St. Catherines Island to kill the two friars stationed there, Fray Miguel, the priest, and Fray Antonio, the lay brother who was his co-worker and interpreter. The chief informed Fray Antonio, offering a canoe and rowers to take the friars to safety at the heavily Christian San Pedro (now Cumberland) Island. Antonio did not believe the warning, or perhaps he simply would not flee the crown of martyrdom. On September 17, the war band arrived on St Catherines, and the friars knew their fate. Fray Miguel offered Mass. Franciscans celebrated that day the Feast of the Stigmata of St. Francis, and the Gospel contained the words of the Lord Jesus, "whoever loses his life for my sake will find it" (Mt. 16.25). For four hours the friars gave themselves to prayer, awaiting the crown of martyrdom. Antonio was the first to receive the blow of the macana, and then Miguel. Their mutilated bodies were left to rot in the sun until crudely buried by faithful Christians at the foot of the great mission cross which Fray Miguel had erected. Later the relics were gathered and taken to the central friary of the friars at St. Augustine, now the National Guard Armory, know as "St. Francis Barracks."
Fray Francisco was the last to die. When the other murders were occurring, he was returning by canoe from St. Augustine to his mission on St. Simons Island. On some unknown date before the end of September, he arrived home with the supplies needed for Mass and for the on-going construction of the mission, and with gifts for his Guale flock. The details of his reception are told succinctly by a chronicler: "They waited for him and when he disembarked, two Natives took him in their arms, while the others came and killed him with blows from the macana. Then they buried him." His Franciscan capuche, or hood, and his sombrero were later recovered from the Guales who were wearing them, but his body was never found.