The division consists of three separate leagues with 16 teams each, two of these leagues consist of teams playing with a license from the Voetbalfederatie Vlaanderen (VFV, the Dutch speaking wing of the RBFA) and one with teams with a license from the Association des Clubs Francophones de Football (ACFF, the French-speaking wing of the RBFA).
In each of the three separate leagues, the season is a regular round-robin tournament with 16 teams.
The winners of each league are directly promoted to the Belgian National Division 1.
The two VFV winners and the ACFF winner are joined by the 13th placed team from the Belgian National Division 1 in the playoff final, with the winner of those four taking the final promotion spot (in case the team from the Belgian National Division 1 wins, this team remains at that level and no extra team from the Belgian Second Amateur Division is promoted besides the three league winners).
On VFV side, a relegation playoff is organised each season between the two teams finishing 14th, with the losing team first in line to drop in case needed, followed by the winner.