The city of Santa Fe was founded in 1610, and El San Miguel (St. Michael's) Mission Church was built between 1610 and and 1628. Foundations of the first church remain observable under the sanctuary of the present structure. Archaeological investigations beneath these foundations reveal evidence of Native American occupation of the site as early and 1300 A.D. In 1680, during the pueblo rebellion, the church vigas in the ceiling were burned, and in 1692 De Vargas ordered the church rebuilt. In 1710 the church was reconstructed and a sacristy was added to its south side in 1714. Repairs to the structure were made between 1798 and 1805 and again in 1830. In 1853 Archbishop Lamy installed the altar stone.
In 1859 the church served as the chapel for the newly arrived Christian Brothers who took over control of St. Michael's School. In 1881 the Christian Brothers purchased the church, a recently completed school building, an adobe building and the land upon which they were situated from the Archdiocese of Santa Fe. Over the years repairs were effected to the roof, walls and floor. In 1955 archaelogical investigations were made, the altar reredos and artwork were restored.