Formed in 1990, Flora were 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.

[3] Flora was founded on 10 March 1990 by Aivar Pohlak as an effort to revive Estonian football during the dissolution of the Soviet Union.

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.

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.

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.

Since 1999, Meistriliiga adopted the current league format with the season running from Spring to Autumn within a single calendar year.

Tarmo Rüütli returned to Flora for the 2009 season, but failed to lead the club to winning the league, placing fourth.

[4] In 2010, Rüütli was replaced by the former Flora player and Estonia national team record cap holder Martin Reim.

Flora successfully defended their title in the 2011 season and won the 2010–11 Estonian Cup, defeating Narva Trans 2–0 in the final.

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.

Under Henn, Flora won the 2019 Meistriliiga and advanced through the first qualifying round of Europa League, beating Radnički Niš 4–2 on aggregate.

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.

[14] 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.

The rivalry began in 1999, when Levadia entered Meistriliiga and immediately challenged the reigning champions Flora for the title, winning the treble in their first year in top-flight football.

The rivalry emerged in the early 2010s, when Kalju started challenging Flora in terms of on-field success, as well as in fan popularity.

Throughout the years, the rivalry has also intensified due to an enmity between Flora's founder Aivar Pohlak and Kalju's president Kuno Tehva.

Flora's signing of Kalju's homegrown players Henrik Pürg and Vlasiy Sinyavskiy in 2018 caused a further strife in the relationship of the two clubs[23] and since then, no transfer deals have taken place between them.

In an interview in 2023, Flora's academy graduate and current national team player Rauno Sappinen said he would rather retire than join Kalju, also calling the rival club 'appalling'.

[25] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.