At the start of the 2008–09 season, Fernandes switched number shirt from number 28 to number 19 after his previous number was taken by Daniel Sturridge. He then scored his first goal of the season against Portsmouth on 21 September 2008, as Manchester City won 6–0. Three days later on 24 September 2008, Fernandes scored his second goal of the season against Brighton & Hove Albion in the second round of the League Cup, as the club lost 5–3 on penalties following a 2–2 draw throughout the 120 minutes match. He found his playing time, mostly coming from the substitute bench after Mark Hughes took over as manager. As the 2008–09 season progressed, Fernandes found himself away from the first team further, due to being on the substitute bench and his own injury concern. At the end of the 2008–09 season, he went on to make twenty–seven appearances and scoring two times in all competitions.