This article is about the club which was known as FC Levadia Maardu between 1998–2004. For its current feeder club, which was known as FC Levadia Tallinn between 2000–2004, see FC Levadia II Tallinn. For Levadia women's team, see FC Levadia Tallinn (women).
In January 2001, Valeri Bondarenko was appointed as a manager. Bondarenko began the season by winning the Estonian Supercup but failed to defend the Meistriliiga title, finishing the season in third place behind the winners Flora and runners-up TVMK. In 2002, Pasi Rautiainen took over as a manager. Under Rautiainen, Levadia finished the 2002 Meistriliiga season second, just two points behind Flora. After the season, Rautiainen left the club and returned to Finland for personal reasons and was replaced by Franco Pancheri. Pancheri coached Levadia for just 9 Meistriliiga matches, before he was sacked due being unable to maintain the level achieved with Rautiainen. In June 2003, Levadia hired former Estonia national football team manager Tarmo Rüütli and finished the season in third place.
Under Prins, Levadia won two consecutive Meistriliiga titles in 2008 and 2009 and an Estonian Cup in 2010. In August 2010, Prins was sacked due to disagreements with the club's board and replaced by Levadia II manager Aleksandr Pushtov. Levadia finished the 2010 season second behind Flora. During the 2010–11 winter transfer window, Levadia lost several key players, including Estonian international players Tarmo Neemelo, Eino Puri and Vladimir Voskoboinikov. In July 2011, Pushtov was sacked after disappointing results in the Meistriliiga and the Champions League and replaced by Sergei Hohlov-Simson. Levadia finished the 2011 season in fourth place, lowest since the club was promoted to the Meistriliiga.
In January 2012, Marko Kristal was hired as a manager. Levadia won the 2011–12 Estonian Cup and finished the 2012 Meistriliiga season in second place behind Nõmme Kalju. Under Kristal, Levadia won the Meistriliiga title in 2013 and defended the title in 2014, while Igor Subbotin scored club record 32 goals. Levadia failed to defend the title in the 2015 season, finishing in second place. After the season, it was announced that Sergei Ratnikov will return to Levadia after 15 years and replace Kristal as a manager. Ratnikov's second tenure as Levadia's manager lasted until 11 July 2016, when he was sacked after a 0–1 loss to Pärnu Linnameeskond in the Meistriliiga. He was replaced by another returning manager, Igor Prins.