Regarding the armed forces of the "Jesuit republic" of the Paraguayan Reductions towards the end of its existence:

The Guaraní army had matured beyond recognition since [the defeat of the Brazilian slave-catchers at] Mboreré. Although it had been hired by Buenos Aires to fight English and Danish corsairs, as a military force it had grown a little plump. As a pageant, it was superbly fluffy. At its head rode the officers in red velvet doublets, trimmed with lace and ostrich feathers. Then came the alcaides [sic?], in short breeches of yellow satin, and the sergeants in scarlet suits and silver waistcoats. The soldiers followed, soaked in color and armed with spears, bolas, and long English guns that needed rests to fire them. They carried the standard of their patron saint before them, to protect them from evil and shot.

[If anyone at Osprey Publishing is listening, I think Indian Soldiers of the Jesuit Republic would make a marvelous addition to your Men at Arms series.]

...In reality, there were few delights for the Guaraní commander, Ñeenguirú's grandson. "King Nicholas" well knew that wars were not won by fine tailoring, and had a premonition of disaster. He wrote his fairwells to the Society: "We are before God as we await are complete destruction...we will resist to the end."

It was not long in coming. Father Ennis stood among the flames and whirling metal, bellowing at his Indians in [execrable] Latin and Irish, but the colonial artillery was overwhelming. In the last set-piece, many of the Guaranís simply crossed their arms and waited for deliverance. In one hour, 1,500 Indians were exterminated. Their surivors took to guerilla warfare, bivouacking in the trees and cutting throats. By 1756, Ennis and King Nicholas were in chains, and the "Jesuit War" was over."

~John Gimlette. At the Tomb of the Inflatable Pig: Travels through Paraguay, p. 288.

Incidentally, in my home town of Tallahassee, once the site of the Franciscan Mission San Luis de Talimali, a native confraternity would often supplement the Spanish garison, marching with their muskets under the banner of Our Lady of the Rosary. It is also instructive to note the establishment of the friary there came at the repeated requests of the Apalachee tribesmen, rather than over their protests.