In 1919, Dr. Christian became Professor of Church History at the Baptist Bible Institute, New Orleans, Louisiana (renamed the New Orleans Baptist Theological Seminary in 1946). He played a major role in the controversies surrounding the restorationist views of Baptist history taught by William Heth Whitsitt (see The Whitsitt Controversy) in the Southern Baptist Theological Seminary of Louisville, Kentucky. He wrote extensive rebuttals to Whitsitt's works and eventually published a history of the Baptists written from a successionist's perspective.
The John T. Christian Library of the New Orleans Baptist Theological Seminary is named in his honor. According to the seminary, "The basic collection came from the library of the outstanding church historian, John T. Christian, who was the first librarian of the seminary. He gave the school his personal library of 18,000 volumes when he joined the faculty in 1919." His personal papers are housed in the Archives at the John T. Christian Library, on campus at the New Orleans Baptist Theological Seminary.
His work is highly acclaimed and recommended by those who are considered scholars in the area of Baptist history.