Ahead of the 2006–07 season, Moore faced uncertainty over his future at Aston Villa following a new ownership. Eventually, his future at the club was resolved following talks with new Manager Martin O'Neill. He scored his first goal of the season, in a 2–0 win against Newcastle United on 27 August 2007. Moore then scored his second goal of the season, in a 2–0 victory over Charlton Athletic on 23 September 2006. At the start of the 2006–07 season, he was featured in the first team for the first eight matches of the season. Moore sustained a serious injury to his right shoulder in a game against Chelsea, an injury which had been persistent during his career. Moore travelled to the US to undergo surgery in October 2006, with Cleveland Browns' head team physician Anthony Miniaci carrying out the procedure, following advice from Aston Villa chairman Randy Lerner. After spending three months on the sidelined, he returned from injury, playing in a behind close door match against Walsall on 24 January 2007. Following this, Moore appeared in a handful matches in the club's reserve to regain his fitness. He even rejected a loan move to a Championship club, preferring to regain his fitness at the club's reserve side instead. Moore returned from his shoulder injury on 9 April 2007, coming on as a substitute for Shaun Maloney against Wigan Athletic at Villa Park. On 14 April 2007, having again come on as a substitute, he scored with a header in a 3–1 win against Middlesbrough at the Riverside Stadium. Moore came on against Bolton Wanderers in the last Villa game of the season to equalise in the 83rd minute, earning Villa a draw. At the end of the 2006–07 season, he went on to make fourteen appearances and scoring four times in all competitions.