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FS Metta was officially founded on May 2, 2006, though the club had been active in youth tournaments since 2000. In 2007 FS Metta and University of Latvia (Latvijas Universitāte) merged as a senior professional team and participated in the Latvian Championship first division (Traffic 1. līga). They finished the season in the fourth position. The club remained at the same level for the next four seasons. Though a professional club, Metta retained the prefix FS (Futbola Skola), since their policy was to invest in youth players. In 2011 Metta won the Latvian First League championship and were automatically promoted to the Latvian Higher League – the top tier of Latvian football.
The affiliation with the university provides the club with a greater financial backing and the players with the opportunity, if wanted, to study at the most prestigious Latvian University. The club was created with the aim to gather the greatest youth talents from across the country and surrounding areas to build and shape them into expensive players for sale to bigger clubs.
In 2020 FK Metta were the youngest top-tier team in Europe. At the end of the season, the team's average age was 19,5.
In September 2020, FK Metta forward Raimonds Krollis made his debut for the Latvia national football team. He became the first-ever player that has gone through the whole FK Metta academy and played for the Senior national team.

