Kirchhoff made his Bayern Munich debut, coming on as a 61st-minute substitute, as the club won 5–0 in the team's 2013–14 DFB-Pokal first-round game against Schwarz-Weiß Rehden. Four days later on 9 August 2013 he made his league debut for the club, coming on as a 73rd-minute substitute, in a 3–1 win against Borussia Mönchengladbach in the opening game of the season. However, his return was short–lived when Kirchhoff suffered a muscular problem that kept him out throughout August. It wasn't until on 14 September 2013 when he returned to the first team, coming on as an 86th-minute substitute, in a 2–0 win against Hannover 96. A month later on 2 October 2013, Kirchhoff made his UEFA Champions League debut, coming on as a 76th-minute substitute, in a 3–1 win against Manchester City. However, he found his first team opportunities at FC Bayern Munich limited, resulting in him being placed on the substitute bench and faced his own injury concern. By the time Kirchhoff left the club, he made eleven appearances in all competitions. Despite being loaned out, Kirchhoff was a member of Bayern Munich squad that won the Bundesliga and FIFA Club World Cup.
