After attending Saint John"s Academy in Rensselaer, he studied at Mount Saint Mary"s College in Emmitsburg, Maryland, from where he obtained a Bachelor of Arts degree in 1899 and a Master of Arts in 1901.
He was ordained to the priesthood on February 27, 1904. He then served as a curate at Saint Peter"s Church in Troy until 1909, when he became spiritual director of the Pontifical North American College in Rome. In 1912 he earned a Doctor of Sacred Theology.
On May 24, 1922, Mahoney was appointed Bishop of Sioux Falls, South Dakota, by Pope Pius XI. He received his episcopal consecration on the following June 29 from Cardinal Gaetano de Lai, with Bishops Giovanni Maria Zonghi and Giacomo Sinibaldi serving as co-consecrators, in Rome.
He remained at Sioux Falls for the next sixteen years, until his death at age 63.