The design for the church of St. Margaret Mary is inspired by the mission churches of the American Southwest and Mexico. The new church is located on a plateau next to the existing parish buildings and can be seen from a long distance. The exterior of the church is finished in white stucco with a clay tile roof. A bell tower rises on the south side of the church, set back slightly from the front facade.
From Oatman Road, the new church is approached on axis with a courtyard. The courtyard is landscaped with native desert shrubs and cacti and has a fountain at the center. It is enclosed on two sides by an arcade, behind which are placed support spaces such as the robing sacristy, restrooms and the gift shop. The facade focuses on a richly carved stone entry arch topped by an ornate window above. Niches flank the entry, with statues of St. Joseph to the left and the Blessed Virgin with Child to the right.
From the courtyard, one enters into a generous narthex, from which stairs and an elevator to the choir loft can be accessed. The church is cruciform in plan with a nave, side aisles, and a transept. The baptismal font is placed near the entrance to the nave on the south side of the main aisle. An exposed wood truss ceiling crowns the nave and transepts. Stations of the cross adorn the walls in the side aisles. The transept arms contain shrines dedicated to Our Lady of Guadalupe (south) and the Sacred Heart (north). Opposite the large shrines, smaller niches contain statues of St. Lorenzo Ruiz and St. Jude. The church seats 960 people in the nave and 50 people in the choir loft.
The sanctuary, located in the crossing, is raised to give it prominence and good visibility from all seats in the church. The marble altar is placed under a baldacchino and the tabernacle is placed at the center of an ornate retablo in the apse. At the center of the retablo is a life-size crucifix flanked by images of St. Margaret Mary and St. Peter.
