An elevated plain above a narrow estuary at the mouth of the Río San José gave early Spanish settlers protection from pirate raids and uprisings by indigenous peoples. The first Jesuit missionaries arrived in 1730 from settlements to the north and tried several sites before choosing the current town center as the permanent location for a mission.

Surrounded by huertas, modern-day San José consists of a historic downtown with an attractive plaza and church as well as many restored colonial buildings. The newer part of town includes a nine-hole golf course and beachfront hotel zone. There is also a busy commercial area along Mexico 1.

The town is the municipal seat for Los Cabos. Many expats, especially artists, have taken up residence in San José in recent years, but for the most part they seem committed to restoring and preserving their adopted community of Josefinos, and so far the town retains an authentic Mexican feel.