The soldiers' quarters were situated along the fourth side, positioned behind the church. This location was designed to provide a defensive perimeter and offer accommodation for the military personnel stationed at the mission.
The missions were among the strongest fortifications built in Texas.

At Mission San José, the soldiers' quarters were a key part of the mission complex, located within the fortified compound. These quarters provided living space for the Spanish soldiers who protected the mission and its inhabitants. The quarters were part of a larger mission community that also included native family quarters, a granary, and a grist mill.