After the turn of the century, Levadia moved their home matches from Maardu to the Kadriorg Stadium[3] and managed to repeat their success by winning another treble during the 2000 season.

Levadia failed to defend their title, finishing the 2001 season in third place and in November 2001, Bondarenko was replaced by Pasi Rautiainen.

In March 2008, Rüütli was hired by the Estonian Football Association to coach the Estonia national team and his assistant Igor Prins took over as manager.

In August 2010, Prins was sacked due to disagreements with the board and replaced by Levadia II manager Aleksandr Puštov.

In July 2011, Puštov was sacked after disappointing results in the Meistriliiga and the Champions League and replaced by Sergei Hohlov-Simson.

Following another second-place finish in the 2017 season, Levadia announced they will merge with FC Infonet Tallinn, the Estonian champions of 2016.

FCI Levadia finished the 2018 season as runners-up, but won the Estonian Cup, beating rivals FC Flora 1–0 in the final.

On 15 September 2019, Rogić was sacked after disappointing results, with assistant coach Vladimir Vassiljev taking over as caretaker manager.

In November 2019, former Estonia head coach and record cap holder Martin Reim was appointed as manager.

However, after a disappointing start to the season, Martin Reim decided to resign in July 2020 and Vladimir Vassiljev took over the role.

In August 2020, Levadia's former assistant coach Marko Savić returned to the club and became joint managers with Vassiljev.

In July 2022, Marko Savić and Vladimir Vassiljev announced they will be stepping down as head coaches of the club, with the main driver for the resignation being the disappointing 1–6 loss against Víkingur Reykjavík in the UEFA Champions League preliminary round.

[1] Levadia uses Sportland Arena artificial turf stadium for training and home matches during winter and early spring months.

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.

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