 When Neale returned to the United States in 1788, Bishop John Carroll assigned him as pastor of the church at St. Thomas Manor, where he aligned himself with the rural clergy in opposing to Carroll's founding of Georgetown College and attempted reform of the rural manors; his conflict with Carroll over various issues would continue for much of his life.In 1790, Neale became the first pastor of the Georgetown Chapel, which would become Holy Trinity Church, the first Catholic church in Washington, D.C.Overseeing its construction and the rapid growth of its congregation, he would remain pastor for 27 years.