Since the early years of the clubs formation they have often had an academy to some degree with the focus of developing youth players for the first team.

In 2010 Lechia Gdańsk and Grupa Lotos set up the Akademia Piłkarska Lechia Gdańsk (APLG) (English: Football Academy Lechia Gdańsk) meaning that development of youth players could be done away from the club itself, a decision which meant the club could focus more on the first team and because it was expected that it would be easier for the academy to get addition funds if it was not totally connected to the club.

Currently Lechia have partnerships with the Rotmanka Football School, APK Jedynka Kartuzy, GAP Sparta Gdańsk, and Unia Tczew.

As of the 2019–20 season, Lechia II are playing in the "IV liga Pomerania" league, the fifth tier of Polish football.

[15] Shortly after reforming the second team, the club had issues relating to training pitches and where a stadium where league matches could be played.

Due to being unable to find a suitable ground to play matches at, Lechia II were disbanded for the 2022–23 season.