At the main entrance, the large wooden doors hint at the Spanish influence that is felt throughout the chapel. Having spent a year in Spain and several years in Mexico, Mr. Kibbey, the architect, had a genuine feeling for the heritage of the Catholic Hispanic Southwest.

The interior of the chapel combines much of the Catholic spirit of Andalusia in southern Spain and the 18th century church architecture found in different parts of Mexico. The Spanish Colonial architecture is more restrained than the flamboyant baroque of the numerous period churches of Mexico, but is more sophisticated than that of the mission churches of southern Arizona, New Mexico and California.

Upon entering the Chapel, one’s first impression after leaving the brightness of the Arizona sunlight is similar to that of entering the dim cathedral atmosphere of a European church. The filtered light of the stained glass windows tones down the brilliantly painted ceiling of Spanish design — the Moorish influence that is seen in so much of the Catholic church architecture of Spain.

The first point of interest is the pinkish tufa stone altar, designed in the Mexican Baroque style. Cut from a quarry near Wickenburg, this Arizona volcanic stone was carved by local sculptors. Effectively framed above the altar is a painting of the Holy Family. This is the work of a fine (although unknown) artist of the Italian school of Andrea Del Sarto in the 15th century. The central statue of the Sacred Heart is flanked by those of St. Ignatius Loyola, founder of the Society of Jesus, and his companion, St. Francis Xavier, patron of Brophy College Preparatory. The wood-carved legs of the movable altar are the recent works of Taiwanese craftsmen, in duplication of the original ornate pedestals over the doors entering the sacristies.

The large crucifix on the right is an outstanding specimen of art by a wood carver of Rome. The sacristy to the left of the altar features an article of historic interest, a large wooden crucifix carved in about 1670. It came from the Monk’s Cemetery at Evaux near Montfaucon in France, and was a survivor of the World War I battle of Verdun.

The abundant use of sea shells in the chapel — carved into the main altar and decorating the wall lights under the windows — is very common in Spanish Colonial architecture. The tradition has its origin in the shells of St. James (Santiago de Compostela).

The heavy and intricate wrought-iron chandeliers are of pure Spanish design but are the handiwork of a local blacksmith shop. Transverse structural I-beams, encased in wood, carry the weight of the ceiling; the length-wise beams are of solid pine. Small sections of the latter, recently found in the attic, provide an entrance to the Baptistry at the rear of the chapel. A small section of the original communion rail, removed after Vatican Council 11, stands at a side altar dedicated to St. Ignatius.

The painting on the wall of the Baptistry, depicting the history and growth of Phoenix, is the work of Michael Tang, a Brophy student who became a member of the Jesuit Order. The coat of arms of the Society of Jesus over the southeast chapel exit and the seal of the Society of Jesus over the back exit are more recent works of craftsmen in Taiwan. The statue of St. Francis Xavier in the vestibule is the work of a wood carver in Rome.

The structure of the chapel is made of brick and cement mixed on-site. Its tower, 135 feet high, is perfectly proportioned, a desert landmark then and now. The fountain in the front patio was built and donated by the A.F. Wasielewski Company in memory of their founder. The original cast-iron statue of St. Francis Xavier that was installed over the fountain was destroyed in a wind storm. The present cast-stone statue was installed in 1966.

The laying of the cornerstone on April 29, 1928, brought together in Phoenix “probably the greatest assembly of Roman Catholic church dignitaries ever to gather in Arizona.” Also present were many leaders of the city, county, state and federal governments.

An outstanding feature of Brophy Chapel is the series of stained glass windows, designed and executed by the artists of An Tur Gloine (Gaelic for “Tower of Glass”) of Dublin, Ireland. (The artists were also known as The Co-Operative Stained Glass and Mosaic Works, Ltd.) Miss Sarah Purser, a friend of Mrs. Brophy and a member of the Royal Irish Academy, organized and directed several of the famous Stained Glass Guild workers, permitting the artists to design their windows individually.

They are called “jewel” windows, featuring symbols, in distinction from “figure” windows. As far as is known, in the United States, only three other institutions feature these Irish windows, all on the Eastern Seaboard. At the time of Mrs. Brophy’s death in 1934, only one window, the one in the choir loft, had not been ordered. In 1985, Mr. William Lupkin, a Scottsdale artist, was commissioned to design and execute this last window.

The windows portray the symbolism of the articles of the Apostles’ Creed.

The chapel's stained glass windows were removed, cleaned and repaired in a project completed in September 2017.

• Marble baptismal font: Donated by The Ladies Sodality (1947)
• The Holy Family painting: Donated by the Count and Countess Minotto
• Pipe Organ: Donated by Mrs. Robert Kelley
• Stations of the Cross by A. B. Clausen: Donated by Mrs. Virginia Rempe with frames made and donated by Mr. Ray J. Becker.
• Side altar statue of the Blessed Virgin Mary: Donated by Mr. and Mrs. Bernard Hughes
• Side altar statue of St. Ignatius: Donated by Mr. and Mrs. Norbert Sinski
• Antique Crucifix: Donated by Mr. James S. Douglas
• Altar drapery: Donated by Mr. Rory Brophy
• Statue of St. Joseph: Donated by Mr. and Mrs. David Vienna
• Stained glass windows in the vestibule: Designed, created and donated by Scottsdale artist, Mr. William Lupkin
• Restoration of original stained glass windows: Donated by Brophy Mothers' Guild (1985)
• Stained glass window in choir loft: Donated by the Bayless Families

On December 19, 1928, a few months after the buildings were completed, St. Francis Xavier Parish was established as the second parish in Phoenix (St. Mary’s was the first). The Brophy Chapel, designed to serve Brophy's students, served as the parish church until 1959.

Bishop Gercke named the parish’s boundaries as Virginia Avenue to the south, 19th Avenue on the west, 16th Street to the east, and the southern side of the mountains on the north. But he asked the Fathers temporarily to consider their parish extending "west to Glendale, east to Scottsville (sic), and north to the mountains."

Weddings are now performed in Brophy Chapel only when either the groom is a Brophy graduate or the bride is an alumna of Xavier College Preparatory.