After a career in which he collected three Olympic and two World Championship medals, Bauer confirmed his retirement from competing for the Czech national team after the 2017 Nordic World Championships in Lahti, although he indicated that he would continue competing in long-distance races for his own team, which he had set up three years previously. In April 2019 he was named as the Visma Ski Classics Pro Team Director of the year for his work with his ED System Bauer Team. The following month, he was announced as head coach of the Polish men's cross-country ski team.