Padre Kino first celebrated Mass at Tumacácori underneath a ramada, or brush shelter, built by the Pimas who were living here.  At that time, the native village was located on the east side of the Santa Cruz River.  Although he designated Guevavi to be the cabecera, he and Fathers Campos and San Martín continued to visit Tumacácori, sing the Mass, and perform other labors among the inhabitants.  By 1695 an adobe house had been built in the village.  The Padre stayed there during his visits.  He also used the house as a sanctuary for the celebration of Mass, baptisms, and marriages.  However, there is no record of a church having been built on the east side of the river.

In November of 1751, the Pimas rebelled against the Spaniards and the resulting conflict, though it lasted less than a month, caused the abandonment of Tumacácori for over a year.  When everyone returned, however, the Spaniards had started construction of a presidio at Tubac.  The village of Tumacácori was moved to the present location to be near to, and on the same side of the river as the new presidio.

All that remains of the church that was begun that spring of 1753 is the foundation.  The date of its completion is uncertain, but it is known to have been in use by the summer of 1757, just four years later.  Lorenzo, the alcalde, was buried in the church in 1757.  The Jesuits used this small church for ten years, until their expulsion in July of 1767.  Father Custodio Ximeno was the last Jesuit to serve at Guevavi-Tumacácori.  He performed his last service here on June 14, 1767, just six weeks before his arrest at Guevavi and his subsequent exile.  A year later the Franciscans arrived on the scene.  They continued to use this building until the completion of their new church in 1822.