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The historian James T. Campbell wrote of Payne in his ''Songs of Zion: The African Methodist Episcopal Church in the United States and South Africa'' (1995): "No single individual, with the possible exception of Richard Allen himself, did more to shape the trajectory and tone of African Methodism."
* Daniel Payne College, a historically black college that operated in Alabama from 1889 to 1979, was named in his honor. After the college closed, the city of Birmingham renamed a street Daniel Payne Drive.
* Payne Theological Seminary in Wilberforce, Ohio, is named in his honor.
* A Pennsylvania State Historical Marker was installed in his honor at 239 N. Washington St. at Gettysburg College, recognizing his study there.
* Payne is celebrated on the Lutheran liturgical calendar
* Payne elementary school in Washington, DC, is named for him.