Following his playing career, Siebert became head baseball coach at the University of Minnesota, leading the team to College World Series titles in 1956, 1960 and 1964. He died at age 66 in Minneapolis, Minnesota.In 1948, Siebert took over as head coach of the Golden Gophers. The "Chief" would go on to become one of the greatest coaches in college baseball history and helped develop baseball at all levels in Minnesota. By the time his career had ended in Gold Country, Siebert had become the winningest coach in Gopher history with a 754–361–6 record and a .676 winning percentage. He sent five different teams to the College World Series and, of course, he brought home three NCAA titles in 1956, 1960 and 1964. His teams also captured 12 Big Ten titles. Amazingly, he endured only three losing seasons.
In addition to coaching the Minnesota Gophers, during the 1950s Siebert was a player/coach for the Litchfield Optimists, the Willmar Rails, and the Minneapolis Kopps Realty teams in Minnesota amateur Town Team Baseball. This arrangement allowed Siebert to evaluate talent and coach his Gophers players during the collegiate off-season.
Siebert served as the president of the American College Baseball Coaches Association. Among his many honors and accolades, Siebert was twice named as college baseball's Coach of the Year; is a member of the College Baseball Hall of Fame; and was a recipient of college baseball's highest award, the Lefty Gomez Trophy, which recognizes an individual who has made an outstanding contribution and given service to the development of college baseball.