The same year, the club joined J.League Division 2, the second-highest flight in Japanese football (renamed to its current name of J2 League in 2015) and placed third.

[3] In the 2009 season, Ōita suffered their worst-ever results in their seven-year history in the topflight, including 14 straight losses in league matches, which is the current worst record in the J.League since the golden goal system was eliminated.

[5] During the 2012 J.League Division 2 season, Ōita finished in sixth place, qualifying for the promotion playoffs in the first year of its introduction in Japan's second flight as the club had also paid back all its emergency loans that October.

After finishing 18th in 2021, Trinita would be relegated back to J2 League, but in the background of that, the club made a Cinderella run to the Emperor's Cup Final.

Just 1 week after the confirmation to be relegated, they defeated defending Emperor's Cup champion Kawasaki Frontale in stunning fashion in the semis; after the game was tied 1 all, Trinita won 4–5 on penalty kicks.

The club's home ground is Resonac Dome Oita, also known as the "Big Eye", which was one of the venues built for the 2002 FIFA World Cup.