In the 2006–07 season, Gilardino's scored his first UEFA Champions League goal on 1 November 2006, in a 4–1 win against Anderlecht. His European offensive output the next season was equally disappointing, with only two goals. However, one of his two goals helped Milan seal a decisive 3–0 win over Manchester United in the second leg of the semi-finals on 3 May 2007, which put them back into the Champions League final and set up a rematch with Liverpool. He played only two minutes as a substitute for Filippo Inzaghi in Milan's 2–1 victory.