St. Michael’s began as a parochial mission of St. Philip’s in the Hills Episcopal Church. At a vestry meeting in February 1953, the Reverend George Ferguson, Rector of St. Philip’s, announced his intention to begin construction of a church on a lot opposite of what then was the end of Fifth Street on unpaved Wilmot Road on property belonging to Harold Bell Wright Estates, formerly the property of the well-known novelist. This parcel, which was being developed as a residential subdivision, was made available to St. Philip’s by several owners of the estate for the purpose of building a church.

John Clinton Fowler, the rector of St. John’s Episcopal Church, Bisbee accepted Rev. Ferguson’s invitation to become the first vicar of the new parish chapel. A native Arizonan, born in Douglas, Fr. Fowler attended public schools in Tucson. His college career at the University of Arizona was interrupted by military service overseas in WWII. After returning from the War and graduating from U of A, Fr. Fowler attended the General Theological Seminary in New York.

Fr. John R. Smith was elected and installed as the current rector in February of 1996. Under his direction, a middle school addition was added in 1997. A new pipe organ chamber, for the Aeolian-Skinner pipe organ, at the north of the high altar, designed by Bob Vint and organ restoration by Grahame Davis, was in place in 1998. During the year 2000, along with the parish center, Mulvaney kitchen and five classrooms at the east side of the historic courtyard was in place. Since 2000, the labyrinth has been installed near the parish center, used by all for contemplation meditative walks. In 2003, a new student center, new and replacement classrooms, and a science center was designed by Bob Vint and constructed by Cobre Building Systems. Currently, there is work being performed to install the fifth and final section (antiphonal) to the pipe organ at the present choir loft location.