Pueblo Revolt or Pope's Rebellion took place in 1680 when the indigenous people in this region (within the current territory of New Mexico), rose against the Spanish colonizers. They were able to expel most settler and almost half a thousand Spanish were killed there, even tough 12 years later the Spanish came back and where able to recover powe over this territory again.
The Franciscans had established in the region to fulfil the mission of spreading the Catholic doctrine among the natives. But what they actually did was to supress all remainings from the prior beliefs of the indigenous people, which they considered pagan: burnt symbol, destroyed religious buildings, etc.
Hence, in 1680 Pueblo's spiritual leader called Pope, who had been humilliated by the Spanish, started the rebellion against the colonizers. Many Franciscans were killed or mutilated and also their churches were destroyed. The rage was mainly focused on this religious order. This is why they did not slaughter all Spanish people there, and just made them leave their region.