In 1934, Waldorf replaced Bo McMillin as football coach at Kansas State. Waldorf coached K-State for only one season, 1934. They won the Big Six Conference championship, the first Big Six title in football for the school (it would be 69 years, in 2003 when the Wildcats would win their next conference title in the Big 12 Conference).
In 1935, Waldorf moved to Northwestern University, where he remained head coach until 1946. In his very first season at Northwestern, he was named college football's first national coach of the year. In his second season, he took Northwestern to the Big Ten Conference crown. His 12-year mark at Northwestern was 49–45–7. While at Northwestern, Waldorf also convinced future legend Otto Graham to try out for football.