In the beginning of 2010, he announced that he will not play for the national team because he wants to focus on his club career. In 2011, he stated the same. However, after Estonia finished in second place in Group C in UEFA Euro 2012 qualifying in October 2011, Lindpere left the door open to return to the national team for their play-off series against Ireland. He stated that his decision to play would heavily depend on whether his club team qualified for the MLS play-offs and that they were his main priority at the moment. After New York's elimination from the play-offs, Lindpere was given permission to join the Estonia squad for its matches against Ireland.