In July 2009, Larsson scored three goals in the Europa League qualifying ties against Eastern European minnows Mika and Zestaponi. He broke his knee-cap during the first leg of the next qualifying round against Sarajevo on 30 July 2009, and was out for an estimated eight weeks. Some reports at the time suggested that this in fact was the end of his playing career, with this injury also coming on top of the recent death of his younger brother, Robert. However, he returned to the first team on 16 September 2009, appearing as a substitute in a 1–3 defeat against IFK Göteborg in the Swedish Cup, and then on 24 September 2009 in his first start since returning from injury, he scored two goals (including the winner) against league rivals AIK. He is Helsingborg's record goalscorer in UEFA competitions with 12 goals.
On 20 October 2009, Larsson announced his retirement from playing at the end of the 2009 Allsvenskan. The announcement followed a previous statement from the player declaring his intention to retire from international duty. Larsson had also stated his desire to move into coaching and expressed his intent to study for coaching badges in Scotland under the Scottish Football Association system. The announcement quickly sparked rumours of a return to Celtic as manager, even going so far as to suggest a link-up with former Celtic teammate Ľubomír Moravčík as his assistant. Larsson also discussed the possibility of taking up floorball on a full-time basis.
Larsson took to the pitch for the final time in Helsingborg's 2–0 Allsvenskan loss to Djurgården on 28 October 2009, and was given a standing ovation from the crowd.
On 11 October 2009, Larsson once again decided to retire from the national team.
On 14 December 2009 Larsson was appointed manager at Landskrona BoIS, a Swedish second division football club, on a one-year contract.
On 6 June 2009, before Sweden's 1–0 loss against Denmark, Larsson's younger brother Robert, who had a troubled personal life, was found dead in his flat in their hometown of Helsingborg. Henrik was not told until after the match had concluded. Henrik Larsson also has an elder half-brother, Kim.