The ruin which once constituted the convento, or "priests' quarters," has seen much usage, both during the mission era and afterwards.  The original structure is believed to have been built sometime around 1821 and contained five rooms and a cloister. It was designed in an open square with priests' quarters, kitchens, workrooms for artisans, corrals for stock, spaces for storage and industry, schoolrooms for religious instruction and a small chapel. Within the convento walls was also a sheltered garden for plants whose seeds and cuttings had been imported from Europe. The foundation and parts of the walls of the living quarters of the padres, or sala, are of original construction.  Some repair and remodeling were needed to make it usable however.

After abandonment, it was used as a residence by various people.  In 1906 the Fimbrez family lived in the east room and Guillermo Fimbrez Montez was born there.   In 1929, the convento was repaired by George Boundey, the first resident superintendent of the park.  Three buttresses were added to support the sagging south wall.  The walls were repaired and whitewashed and doors, windows, a fireplace and a tin roof were installed.  In 1930 one end of the convento was occupied by the Boundey family and school was held in the other end. In 1932, the convento was used as the monument office and museum - a function it retained until the current visitor center/museum complex was built in 1937.    In 1955 the protective shelter was placed over the ruins.

Probably the most extensive use the convento ever saw when it was part of the mission was when five priests stayed here for eight days while waiting for the Anza Expedition to leave Tubac between Sunday, October 15 and Monday, October 23, 1775.