Morgan moved to Boston in 1859. "He preached for some time to an independent congregation in the Music Hall. ... He was a popular lecturer."
By 1872 he was pastor and property-owner of the Morgan Chapel, First Independent Methodist Church (est1861) on Shawmut Avenue (at Indiana Place) in Boston's South End.
Morgan died in 1884. In his will, he gave the Morgan Chapel "property in trust to the Benevolent Fraternity of Churches (Unitarian), with the understanding and proviso that it should be managed by a pastor appointed by the New England conference" of Methodists.".