Before the start of the 2006–07 season, Jones scored a hat trick against Anderlecht in Southampton's last pre-season game. Meanwhile, in the Football League Championship Jones scored two goals against Birmingham City on 29 November that ended 4–3 to Southampton. On 26 December 2006, he received the first red card of his career for a push on Mark Hudson in the match against Crystal Palace. He scored another two goals against Southend United in a 4–1 win on the last day of the season to ensure a place in the play-offs for Southampton, following this, Jones was injured for the play-off semi-final defeat at Derby County but finished the season with 16 goals.
