Ahead of the 2009–10 season, Lindgren had to have an operation on his left foot shortly before the end of last season. Although he recovered from his injury, Lindgren, however, was not one hundred percent fit. He was included in Ajax’s friendly match against Ajax Cape Town on 4 July 2009 and played in the first half before being substituted, as the club won 3–2. However since returning from injury, Lindgren found his first team opportunities limited, under the management of head-coach Martin Jol. This led to him discuss his future at Ajax, but he wanted to stay at the club to fight for his place in the first team. Lindgren didn’t make his first team appearance until on 22 September 2009 when he started and played 120 minutes against AZ Alkmaar in the second round of the KNVB Beker, as Ajax lost 2–0. Lindgren spent the rest of the year, playing for the club’s reserve team. With his first team opportunities limited, Lindgren was expected to leave Ajax in the January transfer window. But in mid–January, he was called up to the club’s first team for the first time in three months. Lindgren scored his first goal of the season, in a 1–1 draw against NAC Breda on 17 January 2010. Following this, he was told by Manager Jol to stay at Ajax. Lindgren appeared in the next five matches for the club. However during a match against SC Heerenveen on 13 February 2010, he suffered a knee injury and was substituted at half time, as Ajax won 2–0. Following this, Lindgren did not play for the rest of the 2009–10 season, due to injuries. While absent, the club won the KNVB Cup after beating rivals, Feyenoord, 6–3 on aggregate. At the end of the 2009–10 season, he went on to make eight appearances and scoring once in all competitions.