In February 2010, Müller signed a new contract with Bayern Munich through 2013. During the second half of the season, Müller continued to be a regular first-team starter, usually playing in a central striking role due to the availability of other wide players Franck Ribéry and Arjen Robben. In April 2010, he scored the second goal in a 2–1 win against title rivals Schalke 04, and in the penultimate league match of the season, he scored the first hat-trick of his career, in a 3–1 win over VfL Bochum which effectively secured the German title for Bayern. The title was confirmed a week later with a 3–1 win at Hertha BSC, a match which Müller started.
For the season, he played in all 34 Bundesliga matches, starting 29, and recorded 13 goals and 11 assists. Bayern and Müller were back in Berlin the following week, to face Werder Bremen in the final of the DFB-Pokal. Müller started the match and Bayern won 4–0 to complete the domestic double. Müller scored four goals and made two assists during the competition, which made him its leading scorer for the season. Bayern's season ended in pursuit of a first treble, in the 2010 Champions League Final against Inter Milan at Santiago Bernabéu Stadium in Madrid. It was not to be, however, as they lost 2–0, with both goals coming from Diego Milito. Müller was in the starting line-up and had a key chance just after half-time, with Bayern 1–0 down, but his shot was saved by Júlio César. Müller felt particularly disappointed by this defeat, but he ended his first season as a first-team player with 52 matches played and 19 goals in all competitions.
He was back in the senior squad for its next get-together, a training session in Sindelfingen in January 2010, and was named in the squad for the following match, a friendly against Argentina in March. He made his debut in this game in the starting XI at the Allianz Arena, his home stadium with Bayern. He was substituted in the 66th minute for fellow debutant Toni Kroos as Germany lost 1–0.
In October 2010, he was named on the shortlist for the FIFA Ballon d'Or award along with four of his Germany teammates. Reflecting on his World Cup success, Müller said "I basically got lucky, I hit form at just the right time".