At the start of the 2006–07 season, Lindgren continued to establish himself in the starting eleven, playing in the midfield position. He scored his first goal of the season, in a 2–1 win against TOP Oss in the second round of the KNVB Beker on 20 September 2006. In a match against Excelsior on 25 October 2006, Lindgren sent up the club’s first goal of the game, but was sent–off for a professional foul on Sieme Zijm in the 81st minutes, as FC Groningen won 2–1. After the match, he was given a one match suspension, but the suspension was overturned, due to lack of evidence. Following this, Lindgren contributed three more assists for FC Groningen throughout the 2006–07 season. Despite being sidelined on four occasions during the 2006–07 season, he went on to make thirty–four appearances and scoring once in all competitions.