In 1730, Jesuit Padre Nicholas Tamaral founded Mission San Jose Del Cabo. After he prohibited polygamy, a tradition of the local Pericu Indian society, the Indians rebelled and burned the mission, killing Tamaral. The Spanish soon established a presidio, and, in the mid-19th century, turned it over to Mexican nationals.

During the early 20th century, mining in the area decreased, and San Jose Del Cabo lost population. In the 1930s, a few farmers returned to the area, and in 1940 the church was rebuilt.

San Jose del Cabo remained sparsely populated until the Cape began attracting sportfishers and later tourists in the 1970s. Since the late 1970s, FONATUR (Foundation Nacional de Fomento del Turismo or National Foundation for Tourism Development) has sponsored several tourist development projects along the shoreline. Fortunately, the developments have done little to change San Jose's Spanish colonial character. Local residents take pride in restoring the 18th century architecture and preserving the peaceful atmosphere. Today, San Jose Del Cabo is a welcome alternative to the fiesta atmosphere in nearby Cabo San Lucas.