Born in Utrecht, out of wedlock, he was the son of Cypriaan Gerard Berger van Hengst and Johanna Wagenaar.
However, he did not begin to receive a formal education in music until age 13, with subsequent instruction in piano, organ, violin, theory, and composition.
In 1892, he studied with Brahms' friend Heinrich von Herzogenberg in Berlin, specifically taking lessons in counterpoint.
In 1888, he succeeded Richard Hol as organist of Utrecht Cathedral, and earned fame for his skills at organ performances.
His pupils included Peter van Anrooy, Emile Enthoven, Henri van Goudoever, Alexander Voormolen, Leon Orthel, Clara Wildschut, Allard de Ridder, Willem Pijper, Hendrika Tussenbroek, and Bernard Wagenaar.