The people who originally settled at Sandia migrated into the area from the Four Corners area during the 1300's. By the time Coronado and his men arrived in 1540, the pueblo numbered around 3,000 people. In 1617 the Mission of San Francisco was built and in 1680, the people of Sandia were prominent in the Pueblo Revolt of 1680. The Spanish came back in 1681, 1688 and 1692, each time attacking the pueblo and burning the village before being forced back to Mexico by warriors from other pueblos. Those who escaped each attack on Sandia fled to Hopi and resettled in the village of Payupki. After each attack some returned but after the Spanish reoccupation in 1692, they abandoned Sandia for Payupki. In November of 1742, about 440 of the Sandias came back. They petitioned the Spanish governor to be allowed to resettle their former lands but their requests were ignored until they convinced a Spanish priest to submit the documents for them. In 1748 permission to resettle was granted, with the first requirement being construction of a mission. However, that effort was thwarted by Spanish settlers conscripting the Sandias to perform other work on their privately-owned farms.
On May 24, 1762, Governor Tomas Cachupin ordered the Pueblo of Sandia to be completely rebuilt and that no Indians were to be worked as laborers for Spanish farmers until the pueblo and church were completely reconstructed. Then the Sandias were allowed to reoccupy their original pueblo to create a "buffer" against the Navajo, Apache and Comanche who enjoyed raiding the village of Albuquerque. In 1775, Sandia, acting as that buffer, lost 30 people in an attack by the Comanche. The Comanche had also attacked Santa Fe in force. Those events caused Governor Juan Bautista de Anza to lead Spanish militia into Colorado and engage with the Comanche there. The Battle of Cuerno Verde ended with most of the Comanche command structure killed and the power of the Comanche severely reduced. However, between the Navajo, Apache and small bands of Comanche, Sandia was constantly raided until a truce was eventually struck near "Poi Pa Huth" or "Friendship Arroyo" in the Placitas area.