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.

The first structure at the new location was designed in the style of churches in northern New Mexico by architect Josias T. Joesler and was built by contractor John Murphey. The building, entirely of mud-adobe and timber construction, consisted of a church some 90 feet long and 22 feet wide, with lateral wings extending out on either side of the church entrance for a Sunday school, kitchen and offices. The mud-adobe patio wall that forms the southern boundary of the church grounds was also built at that time.

The building was opened and blessed by members of the Tucson clergy as well as a large congregation at 4:00 p.m., Sunday, November 29th. The first congregation consisted of members who had transferred from St. Philip's parish together with people from the east side of Tucson. The church style, at the direction of Rector Ferguson, was one of moderate churchmanship, in the pattern of St. Philip's in the Hills.

In 1955 a rectory, designed by Joesler, was constructed on the southwest side of the property adjacent to Wilmot Road. In 1958 a new wing of rooms was added extending south from the already existing east wing; in 1960 a kitchen, utility rooms, and a large parish hall was added. The buildings were constructed in the style of the original structure by architect Gordon Luepke, an associate of the late Josias Joesler.

By the end of 1956, the congregation was large enough and finances had become sufficiently dependable that independent parochial status was being discussed. The conditions for independence were set and in January of 1957, St Michael and All Angels was incorporated under the Laws of Arizona as an independent, self-governing parish of the Episcopal Missionary District of Arizona. Fr. Fowler was elected and installed as the first rector of the new parish. The style of the parish was changed to Anglo-Catholic in churchmanship, while in public matters, the parish was beginning its long career as one dedicated to social reform. The civil rights movement, the farm workers movement, the Viet Nam War, nuclear disarmament, and other public issues have all been addressed over the years. In 1964 the church was enlarged by the addition of a transept at the north end with an apse for the high altar, extending the length of the church to 125 feet. The design was by Gordon Luepke and Ed Morgan. In 1993, the Creswell Courtyard was added.

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.