 Upon his return to Flora, Lindpere quickly established himself as one of the best midfielders in the Meistriliiga and helped his club to win the Meistriliiga in 2002 and 2003.In February 2005, Lindpere was loaned to Bulgarian A Group club CSKA Sofia for the remainder of the season.In September 2006, Lindpere was released from the club after an incident with a 4th referee in a Cup match against Levadia.