Lindgren started his coaching career as player-coach for HSG Düsseldorf between 1996 and 1998. He coached HSG Nordhorn from 2003 to 2009 and won the 2007–08 EHF Cup with the club. He coached Rhein Neckar-Löwen from 2009 to 2010. In addition to his club coaching career, he was assistant coach for Sweden from 2007 to 2008 and head coach from 2008 to 2016. During this time, Sweden reached the semi-finals of the 2011 World Championship and the final of the 2012 Summer Olympics. He became coach of Kristianstad in 2012 and won three consecutive Swedish Championships with the club from 2015 to 2017.