The church's structure supports four domes spanning the length of the basilica. All the domes are compound design with the pendentives, following
Roman architecture, transferring the weight of the roof to the pillars. The dome over the intercept point of the crossover, the nave center aisle and the
apse, is topped with stained glass and features a lantern above the dome to emit light into the nave and sanctuary. The dome located over the altar is topped with a
cupola designed to provide light to the altar. The two bell towers are topped with onion shaped domes, typical of the churches of Bavaria and Austria, where Novatus Benzing, the pastor at the time, and Leonard Darscheid, the architectural consultant, both originated. The towers house four bells which ring daily. The large upper windows depict scenes from the life of the Blessed Virgin Mary, while the lower nave and transept windows depict images of popular saints of the Franciscan Order and of the heritage of the cultures represented in the community at the time (German, Spanish, Irish). According to its National Register nomination, "All stained glass was done by
Emil Frei Art Glass Company of St. Louis. The
Stations of the Cross, cast in high relief on gold background, were made by
Andrew Kaletta Company of St. Louis. The woodwork and pews, all of oak, were made by
Theodore Kuntz of Cleveland." The building was deemed architecturally significant "as the largest, earliest, and most impressive Mission Revival structure in Arizona." ==Basilica==