Thanks the abundant water and the rich soil, rye, wheat, olives, figs, sugarcane, pomegranates, cotton, dates and 500 vine stocks could be cultivated. The first wine picking took place in 1733. San Ignacio was long time the most northern mission on the peninsula and the starting point for all expeditions toward the north. In order to prevent the cultivated lands to be destroyed by floods, dams were elevated along 5 km, of which remains can be appreciated east of San Ignacio. (In 1765 Father José Rotea found an 11-foot skeleton that could have belonged to one of the mythical giants who lived in that region before the Cochimíes.)

The mission passed into the hands of the Franciscans in April 1768. The actual church was completed by Dominican Father Juan Gómez.