On 16 May 2009, Jacobsen played 90 minutes in a 3–1 win against future club West Ham United. He went on to play in the 2009 FA Cup Final, coming on as a substitute at half time for Tony Hibbert where he helped to nullify the threat posed by Florent Malouda down the left wing. Prior the match, he said "It would be a dream come true. When you are a boy, you would like to play at Parken, but to play at Wembley is bigger." Despite making only 13 appearances, Everton were keen to keep Jacobsen, which convinced David Moyes, stating that he deserved a new contract.