In his pamphlet A Plea for Christian Hymns, published while he was at Saint James, Muhlenberg called for a greater quantity and quality of hymns to be available for congregational singing than those published in the first Episcopal Prayer Book. In 1823 he published his own collection of hymns which he began to use at Saint James.
At the request of General Convention Muhlenberg and the Rev. Henry Onderdonk, who later became Bishop of Pennsylvania, prepared a hymn book entitled Hymns of the Protestant Episcopal Church in the United States of America. It was used until 1872. Muhlenberg was the author of five of the hymns.