Müller started the 2018–19 season by starting in the German Super Cup. Müller scored in the first two matchdays in the Bundesliga season. He scored in the second round of the German Cup against SV Rödinghausen. He scored two goals against Fortuna Düsseldorf in the Bundesliga on 24 November 2018. On 12 December 2018, Müller played his 105th Champions League match in a match against Ajax and therefore leveling former club legend Philipp Lahm as the record appearance holder in the Champions League at Bayern. In that same match Müller was sent off for the first time in his career for a straight red card. This resulted in a two-match suspension. On 15 December 2018, Müller made his 300th Bundesliga appearance for Bayern against Hannover 96.