He had been licensed to preach for the Methodist Episcopal Church in 1844. His first assignment was in Hannibal, Missouri. In 1848, frustrated by the segregationist policies of the Methodists, he joined the African Methodist Episcopal Church, an independent black denomination started in Philadelphia. By 1859 he became a deacon in Muscatine, Iowa. In 1861, Cain was called as a pastor at the Bridge Street Church in Brooklyn, New York. In 1862, he was ordained as an elder and remained at the Brooklyn church until 1865.