Problems deepened during the winter of 2003 and Flora had to start the 2004 season without a manager before Anders Süvari, who had coached the team before, returned in summer.

Revitalized, Flora once again challenged the top 3 but missed out narrowly, losing 2–3 in the penultimate round and leaving the team just two points away from the bronze medals.

[1] Flora finished the league third in the 2007 and 2008 season but eventually became champions for the first time in 2018.

They have also been successful in the Estonian Women's Cup, winning the competition in 2013 by defeating league rivals Pärnu 2–0 in the finals.

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