Flora made their debut in the UEFA Champions League for the first time in the 1998–99 season, narrowly losing to Steaua București 4–5 on aggregate in the first qualifying round. The club added another Estonian Cup trophy after defeating Lantana 3–2 in the finals. Since 1999, Meistriliiga adopted the current league format with the season running from Spring to Autumn within a single calendar year. The 1999 season was unsuccessful as Flora placed third. In 2000, Tarmo Rüütli was appointed as manager. Under Rüütli, Flora finished the 2000 season as runners-up, behind Levadia who won the title without a single loss. New stadium and a new era (2001–2009) In 2001, a new era began for Flora as the club moved to the new Lilleküla Stadium and Rüütli was replaced by Arno Pijpers. Under Pijpers, Flora won three consecutive Meistriliiga titles in 2001, 2002 and 2003. In the 2003 season, Flora won the league without losing a single league match, extending their unbeaten run from the previous season to 37, while Tor Henning Hamre scored a record 39 goals in a season. Pijpers left Flora in September 2004, before the end of the 2004 season, and was replaced by Janno Kivisild. The team failed to defend the league title for another season, finishing in third place. The 2005 season was unsuccessful as Flora placed fourth, 26 points behind the league champions TVMK. This was the first time Flora didn't win a Meistriliiga medal since 1992. After the disappointing season, Kivisild was replaced by Pasi Rautiainen. In the 2006–07 UEFA Cup, Flora defeated Lyn Oslo 1–1 on aggregate on away goals in the first qualifying round, before losing to Brøndby 0–4 on aggregate in the second qualifying round. The club finished the 2006 season in third place and placed second in the 2007 season. In 2007, Flora also suffered their biggest margin of defeat in the Meistriliiga thus far, losing 0–6 to TVMK. Flora finished the 2008 season as runners-up, behind Levadia once again, despite amassing 91 points and scoring 113 goals. Tarmo Rüütli returned to Flora for the 2009 season, but failed to lead the club to winning the league, placing fourth. Flora were more successful in the Estonian Cup, winning the trophy in 2008 and 2009. Recent history (2010–present) In 2010, Rüütli was replaced by the former Flora player and Estonia national team record cap holder Martin Reim. Under Reim,