Müller began the 2013–14 season under new manager Pep Guardiola by playing in the German Super Cup. On 5 August, Müller scored a hat-trick as Bayern won 5–0 in the team's 2013–14 DFB-Pokal first-round game against Schwarz-Weiß Rehden. In Bayern's opening 2013–14 Bundesliga fixture, Müller missed a penalty for the first time. Seconds later, the save from the penalty flicked the hand of Álvaro Domínguez which resulted in another penalty which David Alaba converted. After this, Müller stated, "I am still happy to take penalties, but I think David Alaba is the main man for spot kicks for now." He played in the UEFA Super Cup.