Injuries limited Belözoğlu to only 35 Premier League appearances in his subsequent two seasons at Newcastle, in which he scored three goals. On 17 January 2008, in an FA Cup replay against Stoke City, he was sent off after 29 minutes for retaliating after being fouled by John Eustace.
In July 2008, Belözoğlu was unveiled at the Şükrü Saracoğlu Stadium, the traditional homeground of Fenerbahçe, in a signing ceremony. Fanatical Galatasaray supporters started many "anti-Belözoğlu" campaigns for transferring to their rival. However, Belözoğlu stated that he had always been a Fenerbahçe fan, which has been confirmed by some of his past team-mates, including Galatasaray legends Hakan Şükür and Hasan Şaş. After a disappointing first season, consistent performances in the next saw Emre rewarded with the Süper Lig player of the year for the 2009–10 season. He was effective at both ends of the pitch, his experience and combative style proving a valuable asset in taking his team so close in both league and cup. On 3 November 2010, Belözoğlu declared that he hung posters of former Fenerbahçe players Aykut Kocaman, Rıdvan Dilmen and Džoni Novak on his walls at home.