Lindpere played as a midfielder for Nõmme Kalju, Lelle, Flora, Valga, CSKA Sofia, Tromsø, New York Red Bulls, Chicago Fire, and Baník Ostrava.

On 20 August 2009 Lindpere scored against top Spanish side Athletic Bilbao in a 3–2 loss in a UEFA Europa League match played at San Mamés Stadium.

[9] On 21 October 2010 Lindpere scored the Red Bulls second goal in a 2–0 victory over New England Revolution which helped New York clinch its second regular season Eastern Conference title.

[10] On 30 October 2010 Lindpere scored the only goal in the Red Bull's 1–0 victory in the first leg of their First Round Playoff against the San Jose Earthquakes in the 55th minute at Buck Shaw Stadium in Santa Clara.

At mid-season, he was added to the 2010 MLS All-Star roster as an inactive member for the match against Manchester United F.C.,[12] and the end of the season Lindpere was named 2010 Most Valuable Player for New York Red Bulls.

[15] On 26 October 2011 Lindpere helped New York to a 2–0 victory over FC Dallas at Pizza Hut Park in a 2011 MLS Cup Playoffs match by scoring the club's first goal of the night.

Lindpere made his international debut for Estonia on 1 November 1999, when he was 18 years old, in a friendly match against United Arab Emirates in Abu Dhabi, when he substituted Andres Oper in the 46th minute.

[22] 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.

[24] Lindpere gained his 100th cap on 14 June 2015, in a UEFA Euro 2016 qualifying match against San Marino, setting up Sergei Zenjov's opener in a 2–0 home win.