The mission was established in the territory of the Kumeyaay, on the mountainside of the San Solano hills in northwestern Baja California, Mexico.

In that year, the native population had fallen to 40, and the mission was abandoned to the military, who used it as a fort and capital for southern California.

Agricultural crops included wheat, olives, grapes, maize, barley, beans, and other vegetables, all of which were cultivated using irrigation.

Accounts such as those by William Shaler and John Locke, going as far back as 1795, mention trading with the Santo Tomás missionaries.

It is worth mentioning that most of the commerce near San Tomás was illegal because of the Spanish Crown's restrictions against trading with vessels under foreign flags.