Unlike the previous seasons, 2006–07 became Ambrosini's late breakthrough as he had fully recovered from his recurring injuries. Although not an immediate starter at the beginning, following a series of stunning performances, he eventually made his way into the team's starting 11, prompting Carlo Ancelotti to change his preferred formation from 4–3–1–2 to 4–3–2–1 (alternatively, 4–4–1–1), in which he would play a left-sided defensive midfielder, in a role similar to that of Gennaro Gattuso responsible for winning back possession and passing the ball to either a deep-lying playmaker Andrea Pirlo or other attacking players. He scored two decisive goals in Serie A against Sampdoria and Atalanta, both with his head. He was also a key member to Milan's victory over Bayern Munich and Manchester United in the UEFA Champions League, balancing the game for Milan through his vision and leadership skills; his long pass from his team's half of the pitch to an unmarked striker Alberto Gilardino helped ensure Milan's eventual 3–0 victory as Gilardino scored a goal that drastically reduced Manchester United's chances of a comeback. This game also prompted Ambrosini to change his mind about leaving Milan due to lack of playing time and extend his contract until June 2010.