Karl Hoyer studied with Max Reger, Karl Straube and Stephan Krehl at the Conservatory in Leipzig. In 1911, he became as an organist at the Ritter and Domkirche in Reval. In 1912, he became the first organist at St. Jacobi in Chemnitz. As of 1926, he was an organ and theory teacher at the Leipzig Conservatory and, at the same time, a full-time organist at the local Church of St. Nicolai. On November 1, 1932, he joined the NSDAP (member number 1377002). In 1934, he was appointed professor at the Church Music Institute.