At the start of the 2008–09 season, Emanuelson started in the first three matches, playing once in the centre–midfield position and twice in the left–back position before missing two matches due to illness. He returned to the starting line–up against SC Heerenveen on 5 October 2008, and played the whole game, as Ajax lost 5–2. Emanuelson then contributed five assists for the club by the end of the year. On 21 December 2008 he scored his first goal of the season, in a 6–0 win against De Graafschap. By November, Emanuelson began playing in different midfield positions for Ajax. But at one point, he did play in the left–back position against NEC Nijmegen on 18 January 2009, as the club won 4–2. His second goal of the season came on 15 February 2009, in a 2–0 win against rival, Feyenoord. After missing one match due to a stiff neck Emanuelson sustained during a UEFA Cup third round first leg against Fiorentina and set up the only goal of the game in a 1–0 win, he returned to the starting line–up in the return leg against them and helped the side go through to the next round following a 1–1 draw. By March, Emanuelson then publicly criticised Manager Marco van Basten for his substitution policy after he was substituted five times in the last eight league matches. Emanuelson then scored his third goal of the season, in a 7–0 win against Willem II on 12 April 2009. During a 6–2 loss against PSV Eindhoven in a follow–up, he suffered a suspected ankle injury that saw him substituted in the 38th minutes. But Emanuelson was given all clear after the medical team said his injury was not bad as first thought. Despite suffering another injury later in the 2008–09 season, he continued to remain involve in the last remaining matches and scored his fifth goal of the season, in a 1–0 win against FC Twente on the last game of the season. Following this, Emanuelson went on to make forty–two appearances and scoring four times in all competitions.