The mission system that Spain and then Mexico imposed on Alta California was, for the Indigenous people caught within it, a structure of compulsory labor, religious conversion, and demographic catastrophe. At Mission San Fernando, the people who built the structures and worked the fields were primarily Fernandeño (the Spanish name given to the local Tongva), Chumash from the coast to the west, and Tataviam from the mountains to the north. They were brought to the mission — sometimes voluntarily, often not — baptized, assigned to work, and prevented from leaving.

By the mission's peak in the 1810s and early 1820s, several thousand neophytes, as the baptized Indigenous people were called, were living and working at or near Mission San Fernando. By the time the mission era ended, the population had been devastated by European diseases, particularly measles and pneumonia, against which Indigenous Californians had no immunity. The mission's burial records document thousands of deaths. The physical mission — the long low building that still stands — was built by these people, and it stands partly as a record of their presence and what was done to them.

Mexican independence in 1821 set in motion a political process that would end the Franciscan missions. The Secularization Act of 1833 transferred mission lands to civilian and Indigenous control — in theory. In practice, most mission lands were distributed to ranchers through the land grant system, and the missions themselves fell into disuse and then ruin. Mission San Fernando was secularized in 1834. For the following decades, the buildings were used variously as a granary, a hog farm, and a stage stop. The roofs collapsed. The walls crumbled.

The property was returned to the Catholic Church by presidential order in 1861, but recovery was slow. A 1971 earthquake — the Sylmar earthquake, magnitude 6.6, centered just miles away — caused severe damage that required years of reconstruction. The Hearst Foundation funded major restoration work in the 1940s, and subsequent campaigns have worked to preserve what remains.

The convento, the long arcade building used as residence and workshop space, is the largest original adobe structure in California — 243 feet long, with 21 Roman arches along its corridor. That building survived the earthquakes and the neglect better than the church itself, which has been rebuilt multiple times. The church in use today is a reconstruction; the convento is largely original.

Mission San Fernando is an active parish church, which means Mass is said regularly in buildings that have been reconstructed from their ruins. The grounds include the convento and its gardens, the reconstructed church, a small museum with mission-era artifacts, and a cemetery where the remains of many of the mission's workers are buried in unmarked graves.

The surrounding landscape has changed almost beyond recognition. The San Fernando Valley, which the mission once governed as an agricultural estate producing hides, tallow, wine, and grain, is now one of the most densely developed suburban regions in the United States. Freeways run past the mission grounds. The city of San Fernando surrounds the property. And yet the convento's adobe walls remain — thick, earth-colored, cool in the interior even in the summer heat that bakes the Valley floor. They were built to last, by people who had no choice but to build them.