At the start of the 2008–09 season, Samba continued to form a centre–back partnership with Nelsen. However, during a 4–1 loss against West Ham United on 30 August 2008, he scored an own goal in the 20th minutes to give the opposition team a 2–0 lead. Almost a month later on 27 September 2008, Samba was able to make amends when he scored his first goal of the season, in a 2–1 win against Newcastle United. Since the start of the season, Samba started in every matches until he missed out against Middlesbrough on 25 October 2008, due to a concussion. But Samba was able to return to the starting line–up four days later on 29 October 2008, in a 3–2 loss against Aston Villa. Two weeks later on 15 November 2008, he scored his second league goal of the season, in a 2–1 loss against Sunderland. Three months later on 15 February 2009, Samba scored his third goal of the season, in a 2–2 draw against Coventry City in the fifth round of the FA Cup. Although recognised predominantly as a defender, Samba made several appearances as a striker in the latter stages of the 2008–09 season. On 4 April 2009, with Blackburn losing 1–0 against Tottenham Hotspur, he started the second half up front. Blackburn went on to win 2–1, with manager Sam Allardyce claiming Samba's impact as "key to victory." During the next league match against Liverpool at Anfield on 11 April, he again started as a lone striker, with natural striker Benni McCarthy left on the bench. Samba continued to play as a striker in the next match against Wigan Athletic in the 2–0 win for Blackburn. For his performance, he was awarded Performance of the Season at the club’s award ceremony. By the end of the season, Samba had made thirty–nine appearances and scoring three times in all competitions.