The team was founded in 2008. FC Lootos only had girls team, so when girls reached the age of 16, they were forced to leave the club. This new team took the name Põlva F.C. Lootos and played their home games at Lootospark, located in Põlva. It took just one season to gain promotion to the Naiste Meistriliiga, when the club won the Naiste Esiliiga in 2008 under the management of Kaido Kukli and Indrek Käo. From 2009, team played five seasons in Naiste Meistriliiga. After finishing 5th in 2013, club's top goal scoring forward Signy Aarna left the club to play professional football at Finnish team Pallokissat. Club started program for changing players generation and left Meistriliiga. Once more it took just one season to gain promotion to the Naiste Esiliiga, when the club won the Naiste Teine liiga in the 2014. Season 2015 was most successful ever when club reached the final of the Estonian Cups after a 2–1 semi-final win over Levadia at the Lootospark. Allegros were beaten 11–0 by current cup holdersPärnu in the final at the A Le Coq Arena in Tallinn. Team went on to win 2nd place the 2016 Naiste Esiliiga and automatic promotion to the Naiste Meistriliiga, ending their three-year stint in the lower divisions. On the season 2017 team was finishing on the 7th place and 1-1, 0-0 draws against Nõmme Kalju FC on the promotional round secured place on Naiste Meistriliiga for another season. Season 2018 started with Lootos suffering one of the worst results in their history. Losing at first their homeground Lootospark team played first 7 games on away grounds and lose all of them. New home groundTilsi staadion helps team a lot to secure place on Naiste Meistriliiga for clubs 25th anniversary season 2019 and end the season in 6th place
