Regarding the facade as a whole one is impressed with the striking contrast between the blank surfaces of the smooth outer walls and towers, and the concentrated decoration of the few wall openings. Over each of the lower windows in the towers is a delicate relief almost monastic in its simplicity. These windows are grilled with slender wooden spindles in the traditional Spanish manner.
Inside to the left of the nave is the Baptistry and over head the choir loft from which the best view of the interior is obtained. The plan of the vaulted interior is a perfect Latin cross with transepts, apse and nave. The right and left transepts are treated as chapels. At the north end is the chancel with its high altar. Over the crossing of transept and nave, the lofty dome rises over an octagonal drum supported on the arches and pendentives, while to the left and right are richly appointed transept chapels each containing two altars. Light streaming through the high windows in the clearstory and the four medallion windows in the drum of the dome is refracted from wall to wall in soft bluish tones.
The walls of the interior are richly adorned with frescoes and gilded ornament. The interior decorations of San Xavier, though somewhat faded in color are perhaps richer than those of other missions—the elaborate detail of its gilded altars, the bizarre painted statues, the spindled altar rails and wine glass pulpit, are in keeping with the rich traditions of Spain and Mexico.
The sides of the vaulted nave, adorned with frescoes, a painted dado and cornice, are lined with heavily capped pilasters. Frescoes, painted in bold reds, yellows, blues, and browns and outlined in orange and black, recall at once the work of early Spanish painters, the eastern heritage of early Christian art, and at the same time, the hand of a native race attuned to brilliant color. The large frescoes, _The Last Supper_ and _The Holy Ghost Descending Upon The Disciples_, to the left and right respectively, are said to be the work of a monk from the college of Queretaro. The dadoes painted in imitation of tiles have almost disappeared. Below the molded brick cornice is a colorful frieze decorated with the cord and hem of the Franciscan vestments and the traditional fringe of bell and pomegranate.