Morgan made 24 Premier League appearances in the 2006–07 season, scoring once in a 2–1 home win over Charlton Athletic on 2 December. However United were relegated on goal difference after losing 2–1 at home to Wigan Athletic on the final day of the season. He played 30 games of the 2007–08 campaign under Bryan Robson and Kevin Blackwell, and was twice sent off for receiving two bookable offences in wins over Preston North End and Hull City. This took Morgan on to six red cards at the club, giving him the distinction of becoming the club's all-time most sent off player.