On transfer deadline day, 1 September 2008, Aluko returned to Aberdeen on a permanent basis, signing a three-year contract for a fee of £50,000 with the club. He made his return in a 2–1 home defeat to Hamilton on 13 September, and scored his first goal since rejoining the club to clinch Aberdeen's first home win of the season, a single-goal victory over Kilmarnock on 1 November. Aluko went on to win the SPL Young Player of the Month award for November 2008. In September 2009, the tabloid press reported that he had put his Aberdeen Future in jeopardy by going to play in the 2009 FIFA U-20 World Cup, against the wishes of manager Mark McGhee. He left the club at the end of his contract in July 2011.