During the early weeks of the revolt, settlers and missionaries were killed and villages abandoned by fleeing Spaniards. On 13 August 1680, Governor Otermin and approximately one thousand individuals managed to barricade themselves within the walls of the capital in Santa Fe. Anther group of approximately fifteen hundred survivors sought refuge with Lieutenant General Garcia at Isleta.

By 16 August 1680, the number of Pueblo Indians camped outside of the Santa Fe capital had increased to over two thousand. Governor Otermin's Indian servant, Juan, was sent by the Indians to deliver an ultimatum to the Spaniards. Juan entered the gates of the capital with a sash around his waist which had been made from the cloth bookmark of the convent's prayer book. He presented Otermin with a red cross and a white cross. Otermin was instructed by his former servant to choose one of the two crosses. If the white cross was selected, then this would signify that the Spaniards were willing to abandon their New Mexico settlements. Conversely, if the Spaniards chose the red cross, then the Pueblos would interpret this to mean that further bloodshed would be necessary in order to drive out the Spanish. Governor Otermin refused to select either of the Christian symbols and instead berated his former Indian servant for being an apostate. Juan left the capital and returned to his fellow warriors.