I have been reading up (vi Wikipedia) on El Dorado and the Spanish and English expeditions through South America. It seems pretty clear that there were Priests and Scholars who would accompany conquistadors on expeditions through the jungle to "interact" with locals or to "find" treasure and natural resources. See Pedro Simón and Juan de Castellanos
I am assuming that the majority of Spanish priests would have been Catholic.
In general, I would assume that in any combat engagements a priest would typically not participate. I doubt that they would use swords or spears to fight the enemy. I wouldn't be surprised if some had weapons such as a staff, dagger, or pistol for self defense, though I am not very familiar with the Catholic and specifically Franciscan traditions to know if this would be taboo. Even if it was taboo, on the frontiers of South America would priests follow the rules very closely?
I am mostly focused on the time around 1550-1600 in Muisca (Bolivia and Columbia), but I would also be curious to hear about other denominations/times/locations that involve Spanish conquest of the Americas.
Are there documented cases of Catholic priests carrying weapons in self-defense or using them in combat?