Johann Degen was probably born between 1586 and 1588 in Weismain, Upper Franconia (modern-day Germany), the son of a tailor. He probably received his first musical instruction there. In the foreword to his songbook (Gesangbuch) he remembers the choral singing in his native town.
In 1611 he became cantor, or second teacher, in the town of Staffelstein. In 1613 he quit in order to take priestly orders and become chaplain at St. Martin's in Bamberg. He also was organist of the same church for several years (1613 at least until 1616 and later 1624 until 1626) - a highly unusual constellation.
Johann Degen acquired fame through the compilation of a German songbook ("Catholisches Gesangbuch", 1628), reissued in 1670 as the "Bamberger Gesangbuch".
Every melody is printed in four parts, unusual for the time. His last known work was a collection of 53 four- and five-part motets, which he dedicated to the Abbot of Ebrach in 1631.