It was built across the Santa Fe River from the villa proper in an area referred to as the Barrio de Analco, which was inhabited mainly by native people including some Tlaxcalans who had accompanied the Spanish settlers from Mexico.

The original San Miguel Chapel was probably smaller than the present structure, with a rectangular apse, a slightly raised sanctuary, and a simple front elevation with no towers.

When Diego de Vargas led the Spanish back into Santa Fe in 1692, he found the mission burned but reparable.

And having examined it, though of small dimensions, and not for the accommodation of a great number; notwithstanding, on account of said inclemency of the weather, and the urgency of having a church in which should be celebrated the Divine Office and the Holy Sacrifice of the Mass... [I] recognized that it is proper to roof said walls, and to white-wash and repair its windows in a manner that shall be the quickest, easiest, briefest, and least laborious to said natives.

[5]A more thorough rebuilding was undertaken in 1710 under the direction of Don Agustín Flores Vergara, who is named on the main beam supporting the choir loft along with the governor at the time, the Marquis de la Peñuela.

The choir loft is across the width of the chapel over the main door on fourteen round beams which rest on a heavy cross timber.

In 1881, the Archdiocese of Santa Fe sold the little-used building to the Christian Brothers who operated the adjacent St. Michael's College.

This project gave the building a more European appearance, adding arched openings and a pitched metal roof to the front elevation.

The main beam is inscribed: El Señor Marquez de la Peñuela hizo esta fabrica El Alferes Real Don Agustin Flores Vergara su criado Año 1710 The Marquis de la Peñuela erected this building The Royal Ensign Don Agustin Flores Vergara, his servant The year 1710[5] The front elevation of the church faces west and has a central bell tower with a single small window and a larger open void directly above the main entrance.

The wooden reredos or altar screen dates to 1798 and is said to be the work of an unnamed artisan known as the "Laguna Santero" who was active in New Mexico between 1796 and 1808.

A niche in the center of the reredos, with its own small pair of columns, contains a wooden statue of St. Michael the Archangel wielding a sword.

The bell is mostly copper, weighs 780 pounds (350 kg), and bears the legend San José ruega por nosotros Agosto 9 de 1356 Saint Joseph pray for us August 9, 1356[5] The unlikely date of 1356 attracted attention from historians and the public.

This was debunked in 1914 by Benjamin Read, who located an elderly man who remembered the bell being cast in Santa Fe and confirmed that the correct date was 1856, not 1356.