• Fr. Jacob Kunze, Aug. 1853
• Redemptorist priests from St. Joseph in Rochester, 1853-1869
• Fr. Charles A. Vogel, 1869-Aug. 6, 1874
• Fr. Constantin Ulrich, Aug. 6, 1874-June 1887
• Fr. Joseph Netzel, June 1887-1896
• Fr. Herbert Regenbogen, 1896-Jan. 17, 1924 [upon death]
• Msgr. Frederick G. Straub, July 1, 1924-1958 [upon retirement]
• Fr. Francis C. Waterstraat, 1958-1962
• Fr. John M. Merklinger, July 17, 1962-June 25, 1969 [upon retirement]
• Fr. Raymond M. Wuest, June 25, 1969-May 1973 [resigned for health reasons]
• Msgr. Joseph G. Gefell, June 27, 1973-June 23, 1976
• Fr. Edwin R. Wedow, June 23, 1976-June 28, 1978 [Administrator]
• Fr. Clarence W. Gardner, June 28, 1978-June 1986 [upon retirement]
• Foster P. Rogers, June 1986-June 23, 1998
• Fr. Louis A. Vasile, June 23, 1998-June 30, 2015 [upon retirement]
• Fr. Timothy L. Niven, June 30, 2015-June 25, 2019
• Fr. John G. Gathenya, June 25, 2019-June 29, 2021
• Fr. Stephen N. Karani, June 29, 2021-present

On May 5, 1853, approximately 15 German and five Irish families met at Frank's Hotel in the City of Auburn to celebrate the Holy Mass and organize a new Catholic parish. At that time, the only Catholic church in the city of Auburn was Holy Family. This group purchased a property at 100 Wall St., near State St., for $400 to serve as the first St. Alphonsus church. This building was previously a cooper's shop, and originally had been a barn. The early years were a struggle, as the parish had significant financial debt and regular in-fighting between groups of parishioners that required the intervention of Auburn Sheriff department, but over time these problems subsided and the parish grew.

As time progressed, the community outgrew its original church. St. Alphonsus parish purchased a former Millerite-Adventist church on Water St. on Mar. 26, 1861 for $1,900 to serve as the parish's second church building. It took several years to renovate the building, which wasn't completed until 1868. That same year, St. Alphonsus was transferred to the care of the newly-established Diocese of Rochester, previously being a church of the Diocese of Buffalo. Fr. Charles A. Vogel was assigned in 1869 to be the first Diocese of Rochester priest to administer the parish. Under his leadership, a bell tower was constructed, and a rectory was built next to the church. This second church was officially dedicated on Nov. 26, 1871 by Bp. Bernard McQuaid.

Fr. Constantin Ulrich, who was assigned Pastor in 1874, established a temporary parish school in the Auburn Academy of Music on Aug. 6, 1874. In 1886, Fr. Ulrich directed the purchase of land at the corner of Franklin and Seminary Sts. to be the site of a permanent school building. The new school would be completed under the leadership of his successor, Fr. Joseph Netzel, who entrusted the school to the care of the Sisters of St. Joseph on September 7, 1887. The school began with 126 students. During Fr. Netzel's tenure, renovations were made to the church, and two youth societies were formed. In 1888, for the 35th anniversary of the parish, Bp. McQuaid visited and money was raised to purchase stained glass windows and a Christmas nativity scene. The parish had grown to approximately 160 families by 1890.

Fundraising efforts began for a new school building in 1901 as the parish continued to grow. The school was completed and then dedicated on July 29, 1905 by Bp. Thomas Hickey. On April 30, 1907, the parish Holy Name Society began with roughly 100 members. A fire broke out that severely damaged the church on Mar. 11, 1910, resulting in the bell tower and organ being replaced. The church was renovated in 1914, and again in 1921. Renovations were made to the school and rectory buildings in 1924.

Fr. Frederick Straub purchased three lots on Genesee St. on Nov. 3, 1929 to serve as the site of the present-day St. Alphonsus church; which is the third church in the parish's history. The cost of the edifice was over $80,000. After delays caused by severe weather and the Auburn Prison riots, the church was completed and it opened its doors on Dec. 21, 1930. The church was designed by George F. Lorenz of Rochester, who also designed the nearly-identical, though somewhat shorter in length, Our Lady of Mt. Carmel church located in northeast Rochester. Bp. Francis O'Hern performed the dedication.

On July 13, 1933, St. Alphonsus parish purchased land on Owasco Lake to serve as a summer camp for children. The camp would be called "Camp Columbus," and a small chapel was constructed on its property on June 27, 1941 dedicated to Our Lady Queen of Peace. The chapel would remain under the care of St. Alphonsus parish until it closed in the 1960s. The camp and chapel still exist today, though under the ownership of the NYSARC, Inc.

St. Alphonsus parish purchased 103 E. Genesee St. in November of 1938 to serve as a parish house containing two classrooms and a library. On Dec. 7, 1941, in response to World War II, the parish began the "Prayer Front" ministry to pray for those serving overseas in the war. Parishioners would send letters to soldiers, in addition to running clothing and food drives.

The parish once again built a new school beginning in 1949, which was dedicated by Bp. James Kearney on Oct. 8, 1950. A year later, an addition was made to the school that was blessed by Fr. Straub on Aug. 31, 1952. Over 700 students attended the St. Alphonsus school in the early 1950s. Significant growth lead to the construction of a new convent for the sisters in 1962. Five years later, a new parish center was built. The church began its St. Alphonsus Food Pantry in 1972, which still serves the needy to this day.

As the 70s progressed, the parish's growth began to slow down. In 1973, St. Alphonsus school merged with other Catholic schools in Auburn to form the Blessed Trinity school, which was housed in the former St. Alphonsus school building. In December 1987, the parish convent closed and became a rectory for retired priests. In 1996, the school merged again with St. Mary's school and was renamed again as St. Joseph's school.

The church building was completely renovated in 1990 to its present appearance. On Sep. 30, 2000, Bp. Clark celebrated Mass at St. Alphonsus in honor of the 70th anniversary of the current church building. The bishop would visit again a few years later, on May 5, 2003, to celebrate the 150th anniversary of the parish's founding.

St. Alphonsus averages around 600 weekly worshippers today, and is currently under the leadership of Fr. Timothy Niven. The parish has been collaborating with its neighboring Auburn parishes in the face of the present priest shortage to adequately serve the needs of the faithful. The St. Joseph school and St. Alphonsus food pantry continue to serve the community.