He made his debut for the club, coming on as a 33rd minute substitute for the injured Erik Nevland and played for the rest of the game, in a 1–0 win against RBC Roosendaal in the opening game of the season. In a follow–up match, Lindgren scored his first goal for FC Groningen, in a 2–1 loss against RKC Waalwijk. His second goal for the club came on 29 January 2006, in a 3–2 win against NAC Breda. For his performance, he was named Man of the Man by the supporters on the club’s website. On 1 March 2006 it was announced that Lindgren would sign a new deal, making him a FC Groningen player for four years, with the transfer fee reportedly to have cost €300,000. His third goal for the club came on 12 April 2006, in a 2–1 win against FC Utrecht. He then played in both legs of the league’s play–offs spot for the UEFA Champions League for FC Groningen by beating AZ Alkmaar 4–3 on aggregate. However, Lindgren, once again, played in both legs of the league’s play–offs spot for the UEFA Champions League against his former club, Ajax, as the club lost 3–2, resulting in FC Groningen failed to qualify for the UEFA Champions League. Having established himself in the starting eleven for the side, he went on to make forty appearances and scoring three times in all competitions.