On 27 June 2008, Elmander completed a move to Premier League club Bolton Wanderers for an £8.2 million fee, the club's record signing, with the deal including Daniel Braaten moving to Toulouse. Elmander signed a three-year deal, wearing the number 9 shirt by manager Gary Megson.
Elmander's first Premier League goal, a header, came on his competitive debut, against Stoke City on 16 August 2008 in a 3–1 win. Elmander played 30 games in the 2008–09 season, scoring five goals and creating two assists.
From December 2008 to September 2009, Elmander went on a nine-month goal drought, which ended during the League Cup fixture against West Ham United as he scored in extra-time. His first league goal in 11 months came in a 5–1 defeat to Aston Villa.