Founded in 1990, Flora Tallinn was one of the founding members of the Meistriliiga, and is one of two clubs which have never been relegated from the Estonian top division, along with Narva Trans. Domestically, Flora Tallinn has won 9 Meistriliiga, 6 Estonian Cup and 8 Estonian Supercup trophies. In international club football, Flora Tallinn has won 1 Livonia Cup trophy. Flora Tallinn is often regarded to be the flagship of Estonian football due to the club policy of promoting young Estonian players through the ranks and several managers having coached both Flora Tallinn and the Estonia national football team at the same time in the past.
After the first season, the league was reformed to run from autumn to spring, as most of the European top-level football leagues do. Flora Tallinn finished the 1992–93 season as runner-ups with 34 points behind Norma Tallinn, who claimed their second league title with 42 points.
In 2001, a new era began for Flora Tallinn as the club moved to the new A. Le Coq Arena. Rüütli returned to Viljandi Tulevik and was replaced as manager by Arno Pijpers. Under Pijpers, Flora Tallinn won three consecutive Meistriliiga titles in 2001, 2002 and 2003. In 2003, Flora Tallinn won the league without losing a single match and from 2002–03, the team went unbeaten in the Meistriliiga for 37 matches. In 2003, Tor Henning Hamre also broke the club goal scoring record by 39 goals. Pijpers left Flora Tallinn in September 2004, before the end of the 2004 season and was replaced by Janno Kivisild. The team failed to defend the title for another season, finising in third place. Vjatšeslav Zahovaiko won the goal scoring title with 28 goals.
The 2005 season was unsuccessful as Flora Tallinn placed fourth, 26 points behind the league champions TVMK Tallinn. This was the first time Flora Tallinn didn't win a Meistriliiga medal since 1992. After the disappointing season, Kivisild was replaced by Pasi Rautiainen. In the 2006–07 UEFA Cupqualifying rounds, Flora Tallinn 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 Meistriliiga season in third place and came second in 2007. In 2007, Flora Tallinn also suffered their biggest margin of defeat in the Meistriliiga thus far, losing 0–6 to TVMK Tallinn. Flora Tallinn finished the 2008 season second behind Levadia Tallinn once again, despite 91 points and 113 goals scored. In 2009, Tarmo Rüütli returned to Flora Tallinn, replacing Rautiainen as manager but failed to guide the club to winning the league, placing fourth. The club was more successful in the Estonian Cup, winning the trophy in 2008 and 2009.