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The first building at Mission San Francisco was a tule (reed) arbor built by the Spanish soldiers. As soon as the ship San Carlos arrived with supplies in August, construction on more permanent buildings began, and the first buildings were completed by September 1, including a small chapel made of wood plastered with mud, with a tule roof. These buildings were about one-tenth of a mile from the present location.

From 1776 to 1788, four different churches were built, each one torn down because it stood on good soil for farming, and good farm land was scarce. By 1781, the mission settled at its current location, and a wing of the quadrangle was finished.

The current building at Mission San Francisco was started in 1785 and completed in 1791. The flexible structure, with redwood logs fastened together by rawhide strips and wooden pegs, was so sturdy that it survived the earthquakes of 1906 and 1989. The building is 114 feet long and 22 feet wide, with 4-foot-thick adobe walls. Historical records say it took 36,000 adobe bricks to build it.

Inside the chapel, the current tile floor was originally dirt, and there were no seats, but otherwise little has been altered since 1791. The decoration on the ceiling is repainted in the original design, which is taken from the design of the Ohlone men's face paint. The walls were originally painted with designs, too, but they were painted over in the 1950s. On the right wall is a large nineteenth century canvas painting that was once placed in front of the church every year during Easter week.

The altars are all top quality Mexican art. The reredos came from San Blas, Mexico in 1796, and the two side altars, also made in Mexico, were brought to the mission in 1810. The mission's three bells were cast in Mexico in the 1790s and honor saints Joseph, Francis and Martin. The fonts set into the back walls are plates imported from China by way of the Philippines.

There are four marked burial places within the chapel walls: William Leidesdorff, an early Afro-American businessman; the Noe Family; Lieutenant Joaquin Moraga, the leader of the founding expedition, and Richard Carroll, the first pastor after San Francisco became an archdiocese.

After the mission survived the 1906 earthquake, the wooden trusses were paralleled with steel to strengthen it. The historic structure faced its biggest challenge in the late 1990s when wood-eating beetles threatened to destroy it bite by bite. However, through extensive efforts by the mission staff and scientists, the beetles were killed and the mission was saved.

Today, Mission San Francisco is the oldest intact building in the city of San Francisco.