Ahead of the 2008–09 season, Arca switched number shirt from thirty–three to three. However, he suffered ankle injury during a 3–2 win over Hibernian in a friendly match and was sidelined for two months as a result. It wasn't until on 29 October 2008 when he made his return to the first team from injury, coming on as a substitute in the 75th minutes, in a 2–0 win over Manchester City. Since returning to the first team, Arca regained back his first team place, playing in the midfield position over the months. But in mid–January, Arca lost his first team place when suffered an illness that saw him missed one match, followed up by being placed on the substitute bench, as he continued to regain his fitness. Arca made his return to the starting line-up, playing the whole game, in a 1–1 draw against West Ham United in the fifth round of the FA Cup; which Middlesbrough went through in the FA Cup replay by beating them 2–0. Towards the end of the 2008–09 season, he suffered a hamstring injury that saw him out for a month. It wasn't until on 16 May 2009 when Arca made his return to the starting line-up, in a 1–1 draw against Aston Villa. The last game of the season against West Ham United, however, saw them lose 2–1, resulting in their relegation to the Championship in eleven years. At the end of the 2008–09 season, he went on to make twenty–one appearances in all competitions.