He then went south and was licensed to preach. Rev. Keener joined the Alabama Annual Conference of the Methodist Episcopal Church in 1843, and when the church was divided in 1844 remained with the Church, South. He was transferred to the Louisiana Conference in 1848. He was appointed to various churches in Alabama until 1853, when he went to New Orleans where he was Pastor successively of the Poydras Street, Carondelet Street, and Felicity Street churches. He was Presiding Elder of that District in 1858 and 1860, living in New Orleans for twenty years total, all but two years during the American Civil War.