At the start of the 2008–09 season, Lindgren continued to remain as a regular first team player, playing in the midfield position. He scored his first goal of the season, in a 2–0 win against FC Twente on 1 November 2008. A month later, Lindgren captained Ajax in a match against NAC Breda on 12 December 2008 and scored his second goal of the season, in a 3–0 win. However, he suffered a hamstring injury while training and was sidelined for a month. Although Lindgren recovered, he didn’t returned to the first team until on 8 February 2009, coming on as a second half substitute, in a 4–1 loss against SBV Vitesse. Following this, Lindgren made six starts between 15 February 2009 and 8 March 2009. However during a 2–1 loss against Marseille in the first leg of the UEFA Europa League Last Sixteen, he suffered a concussion and was substituted in the 22nd minutes. After the match, Lindgren was taken to the hospital and was sidelined for weeks. Because of his absent, he was no longer used as a vice–captain and was replaced by Thomas Vermaelen. Lindgren didn’t return to the first team until on 12 April 2009 when he came on as a 57th minute substitute, in a 7–0 win against Willem II. At the end of the 2008–09 season, Lindgren went on to make thirty–two appearances and scoring two times in all competitions.