Early history (1990–2000) Flora was founded on 10 March 1990 by
Aivar Pohlak as an effort to revive Estonian football during the
dissolution of the Soviet Union. The team was mainly based on players from Lõvid youth team. Flora finished their
first season in last place and were relegated. The situation changed after the formation of the
Meistriliiga in 1992. After 52 years of the Soviet occupation (
Estonian SSR), Estonian clubs could once again play for the Estonian League Championship title. Flora finished the
inaugural season of the Meistriliiga in fourth place. After the first season, the league was reformed to run from Autumn to Spring. Flora finished the
1992–93 season as runners-up. In 1993,
Roman Ubakivi was appointed as manager. One round before the end of the
1993–94 season,
Tevalte, who led the Meistriliiga table at the time, was controversially disqualified over allegations of match fixing. The season ended with Flora and
Norma both on equal 36 points. Flora won the championship play-off match 5–2 and was awarded their first league title. The club made their
European debut in the
1994–95 UEFA Cup, losing to
Odense 0–6 on aggregate in the preliminary round. Flora managed to defend the league title in the
1994–95 season and won the
1994–95 Estonian Cup, defeating
Lantana-Marlekor 2–0 in the final. lifting Flora's first-ever
Estonian Cup in 1995 In January 1996,
Teitur Thordarson replaced Ubakivi as manager. Disappointing start in the
1995–96 season left the team in second place. Flora finished the
1996–97 season as runners-up once again. In the
1997–98 season, the club won their first league title under Thordarson. Subsequently, the league format was changed and Flora managed to win
another title in the same calendar year. 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. 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. The club also won the
2015–16 Estonian Cup, defeating
Sillamäe Kalev 3–0 in extra time in the final. In May 2016, Aivar Pohlak resigned from the club's presidency and was succeeded by his son Pelle Pohlak. In the first qualifying round of the
2016–17 UEFA Champions League, Flora lost to
Lincoln Red Imps 2–3 on aggregate, after which Hurt resigned and was replaced by
Argo Arbeiter. Flora finished the disappointing
2016 season in fourth place. Arbeiter was sacked and in January 2017, Arno Pijpers returned to take over as manager. In the
2017 season, Flora won their 11th Meistriliiga title. In December 2017, it was announced that Pijpers will not continue as manager.
Jürgen Henn era (2018–2023) is the most successful head coach in FC Flora's history
Jürgen Henn was appointed in Pijpers' place in January 2018. Under Henn, Flora won the
2019 Meistriliiga and advanced through the first qualifying round of Europa League, beating
Radnički Niš 4–2 on aggregate. Flora faced
Eintracht Frankfurt in the second round which brought a record 8,537 people onto the stands in Tallinn, as Flora narrowly lost 1–2 with
Mihkel Ainsalu scoring for the hosts. The second leg saw Flora face the German side at the sold out
Waldstadion, where they were again defeated 1–2 in front of a crowd of 48,000. Despite the result, Flora players were celebrated by the Eintracht fans after the final whistle for their impressive performance, with Eintracht manager
Adi Hütter labelling the scene as extraordinary and touching. Led by Jürgen Henn, Flora won the treble in 2020 by lifting the 2020 Estonian Supercup, the
2019–20 Estonian Cup and the
2020 Meistriliiga title. The club also advanced to the UEFA Europa League qualifying play-offs, where they lost 1–3 to
Dinamo Zagreb on 1 October 2020. in the UEFA Europa League second qualifying round in 2019Flora became the first Estonian side to advance to a
UEFA club competitions group stage when they beat
Shamrock Rovers 5–2 on aggregate to qualify for the
2021–22 UEFA Europa Conference League on 26 August 2021, where they were drawn into group B against
Gent of Belgium,
Partizan of Serbia and
Anorthosis Famagusta of Cyprus. The 2–2 draw away against Anorthosis was the first ever point picked up by an Estonian side in UEFA group stage history, with
Rauno Sappinen scoring both goals as Flora came from 2–0 down to earn a point in Cyprus. On match day 5, Flora made more history by beating Partizan 1–0 in Tallinn, thanks to a goal from
Martin Miller. This result meant that they became the first ever Estonian side to win a game in a UEFA group stage. After finishing the
2021 Meistriliiga season as runners-up, FC Flora won their 14th Estonian championship title in the
2022 season, earning 97 points and thus repeating Levadia's 2009 record of most points in a season. Flora lifted their 15th league title in
2023. On 30 November 2023, Jürgen Henn announced he will be stepping down after six years in charge, marking the end of the longest and most successful managerial tenure in Flora's history.
Recent history (2024–present) Flora replaced Henn with their sporting director and former manager Norbert Hurt, under whom the club started the 2024 season by lifting their 12th Estonian Supercup in February 2024. However in July, Hurt resigned after a disappointing 0–5 home loss in the Champions League first qualifying round and was replaced by the club's U21 head coach Taavi Viik. Flora finished the
2024 season in fourth place, their first outside the top three finish in eight years. The club appointed their recently retired player
Konstantin Vassiljev as head coach for the
2025 season and lifted their 16th league title in Vassiljev's debut year as manager. ==Crest and colours==