The following year a presidio was established at the visita of Tubac, 37 miles to the south, for the protection of San Xavier, its visitas, and the villages of the Christian Indians. Missionary activities were again started and many of the Indians who had previously fled, returned.

In 1767, by Royal Order, the Jesuits were expelled from all Spanish domain. Charles III of Spain, fearing the Jesuits were too persistent in their quest of new lands, decided to replace them with the Franciscan Order. San Xavier, like most of the abandoned missions of the region, was taken over by the Franciscans in 1768. San Xavier came under the direction of Friar Francisco Garcés and before the year was out, while he lay sick at a nearby visita, the mission buildings were destroyed by Apaches.

The padres’ courage and spirit were unshaken however, as we find that four years later a “fairly large” church was erected. The danger from Apache raids became increasingly serious and in 1776, a presidio was established at nearby Tucson for greater protection of San Xavier.

About 1785 two Franciscan friars, successors to Garcés, began work on the building. This evidently was at the site of the present mission. What part, if any, of the present structure belongs to the period of Jesuit occupation is conjectural and there seems to be some confusion at this period regarding the two sites. However, the cruciform (cross-shaped) design of the present structure was not used by the Franciscans for missions and it is reasonable to suppose that the Jesuits may have laid the foundations for the present church, under these circumstances. Also, the name of San Xavier, a Jesuit, was retained, while the Franciscans changed the names of the other Jesuit missions.

The labor of building went on for more than ten years. Except for part of one tower, the structure was probably finished in 1797, as an inscription on the door of the Sacristy indicates: “Pedro Bojs ano die—1797 (Pedro Bojourques—on a day in the year 1797).” The actual building of San Xavier was carried on under the direction of Ignacio Gaona, Spanish architect and master mission builder. Ornaments and fixtures of the older church were placed in the new building.

After Mexico won independence from Spain in 1822, the friars were expelled from the country and the missions were confiscated. San Xavier remained for years without a priest, and the buildings were used for stables, barns, or barracks. At this time the faithful Indians buried many of the ornaments and statues to prevent their destruction in Apache raids.

In 1859, following the Gadsden Purchase, whereby the United States Government purchased from Mexico a large strip of land, San Xavier was brought within the boundaries of the United States. The Arizona missions were put in the diocese of Santa Fe, New Mexico. When the Indians heard that a priest was returning they brought forth the statues and other sacred articles, rang the long silent mission bells and brought their children to be baptized. The church of San Xavier was the only mission not in complete ruin. Extensive repairs were made on the building.

Although the mission withstood the earthquake of 1887, a period of rainy weather caused damage to its walls and ceilings. Restoration work, for the most part by Indian labor, was begun in 1906. Old pictures were studied in an effort to retain the lines of the mission as faithfully as possible. The work was so skillfully done that in many instances it is impossible to distinguish between the old and new construction.

The exteriors of the mission and dependent buildings were newly plastered and the decorations repaired. Some changes were made in the walls of the atrium and in the patio, which had been constructed as a measure of defense against the attacks of Apaches. Additional dormitory and class rooms were constructed. In 1908 the “Grotto of Lourdes,” a replica of the shrine at Lourdes, France, was constructed on the “Little Mountain of the Holy Cross” just east of the mission.

In accordance with the usual custom of the Spanish friars in selecting a building site for a mission, San Xavier del Bac occupies a position in the very heart of the desert, slightly elevated above the surrounding terrain and hemmed in by distant mountains. The majestic mass of the church with its tiny mortuary chapel to the left, its walled atrium fronting a spacious plaza, and its L-shaped dormitory and patio adjoining the church proper at the right, forms an imposing architectural ensemble. The church faces directly south, contrary to the general rule that the apse should be to the east.