In international club football, Flora has won 1 Livonia Cup trophy.Flora was founded on 10 March 1990 by Aivar Pohlak as an effort to revive Estonian football during the dissolution of the Soviet Union.Since 1999, Meistriliiga adopted the current league format with the season running from Spring to Autumn within a single calendar year.Andres Oper, the club's top goalscorer in three previous seasons, left the team in July.Flora managed to defend the title in the 1994–95 season and won the 1994–95 Estonian Cup, beating Lantana-Marlekor 2–0 in the final.In January 1996, Teitur Thordarson replaced Ubakivi as a manager.Flora finished the 1996–97 season in second place behind Lantana once again, while Mart Poom broke the club record by keeping a clean sheet for 756 minutes.
They made their European debut in the 1994–95 UEFA Cup, losing 0–6 on aggregate to Odense in the preliminary round.
Disappointing start in the 1995–96 season left the team in second place behind Lantana.
Lembit Rajala won the goal scoring title with 16 goals.
The situation changed after the restoration of independence and formation of the Meistriliiga in 1992.
After 52 years of foreign occupation, Estonian clubs could once again play for the Estonian League Championship title.