The origins of São José dos Campos lie at the end of the 16th Century when Jesuits founded a cattle farm, Aldeia do Rio Comprido, as cover to avoid raids by the bandeirantes (brave men from São Paulo whose incredible vigour and tenacity in their inland raids in search of gold or to fight Indian tribes greatly contributed to enlarge the Brazilian territory). The Jesuits were then expelled from the land on September 10th 1611 when the law governing indigenous settlements was changed, scattering the remaining villagers.

The Jesuits returned some years later, establishing a settlement on a plateau about nine miles from the original farm. This was the center that gave rise to the city we now know, marked today by the Matriz Church. The climate was pleasant and the position was strategically advantageous for repelling invasions. To all intents and purposes, the mission still looked to outsiders like a cattle farm. This period in the settlement's history saw serious economic privations caused by the outflow of workers attracted by opportunities in the mines.