Arca made his Premier League debut for Middlesbrough against Reading on the opening day of the 2006–07 season; he broke his foot and was substituted at half-time for Andrew Davies. After regaining fitness, Arca made his return to the first team, coming on as a late substitute, in a 1–0 win over Everton on 14 October 2006. With the progress of Andrew Taylor at left-back, Arca had been utilised as central midfielder. He scored his first goal for the club against Charlton Athletic on 23 December 2006. Arca then scored against Charlton Athletic for the second time this season, in a 3–1 win. His third goal of the season came on 17 February 2007, in a 2–2 draw against West Bromwich Albion in the fifth round of the FA Cup; leading to a FA Cup, which they won on penalties and Arca was one of the players successfully convert. He set up an equaliser goal for Lee Cattermole, in a 2–2 draw against Manchester United in the sixth round of the FA Cup; leading to a FA Cup replay once again, which Middlesbrough lost 1–0. However, Arca suffered a groin injury that saw him sidelined for a month. It wasn't until on 28 April 2007 when he returned from injury, coming on as a substitute during the second half, in a 3–2 loss against Tottenham Hotspur. Arca later featured the remaining two matches of the season. At the end of the 2006–07 season, he went on to make twenty–eight appearances and scoring three times in all competitions.