Andy Bayer grew up in Leo, Indiana, and started running cross country and track in the sixth grade. He qualified for the state finals for the first time during his junior year. After a coaching partnership with his cousin Dan Zimmerman, Andy improved dramatically, finishing sixth at the cross country state meet and winning the 3200 to win a state title in one of the closest finishes of all time.

Just shy of a walk on, Andy headed to IU to join its cross country and track teams. By Andy's sophomore year, he had become one of IU's top scorers, breaking the four minute mile, and holding records in the 1500 and the indoor 3000. At IU, Andy was a six-time Big Ten champion and 12 time All-American. In 2012, Andy won the NCAA National Championship in the 1500 in another photo finish. At the national championships that year, Andy was fourth in the 1500, just one spot shy of qualifying for the US Olympic team.