After relegation from the Ekstraklasa, Lechia found themselves back in the II liga. During the 1988–89 season Lechia struggled to adapt to the new league, finishing 10th out of 16. Things failed to improve for Lechia during the next two seasons, finishing both 11th and 12th. The situation slightly improved for Lechia during the 1991–92 and the 1993–94 seasons finishing in 8th before their highest finish of 6th since being relegated. During this period there was a greater rivalry with the three major Tricity clubs, Lechia representing Gdańsk, with Arka and Bałtyk from Gdynia. The 1993–94 season was an important season for the Tricity teams. Bałtyk Gdynia finished highest in the league for the 3rd season in a row, while both Lechia and Arka faced each other for the first time in history in the 1993–94 Polish Cup, with Arka winning the match 1–0. The season was another difficult one for Lechia, in which they finished 14th, 1 place above the relegation zone. The struggles for Lechia reached a devastating end by the end of the 1994–95 season, with the team, ultimately being relegated to the 3rd Division, along with fellow rivals Arka Gdynia.