[2] Following the end of World War II, football in Peja and the rest of the Kosovo region became more prominent and this was in no part due to the rise in tournaments and championships that were held regularly.

The three main clubs that were left in Peja at the time, Besa, Budućnost and Kristal, held a joint assembly early in 1991 and decided to merge the clubs in order to create what is now known as FC Besa Peja that was to compete in the independent League of Kosovo that was organised by the Football Federation of Kosovo, which was out of the Yugoslav football league system.

This parallel competitions were of poor standard and were limited to matches played in remote villages on fields rather since the stadiums were still property of the clubs which were competing in the Yugoslav leagues.

Until 1996 the Kosovo Superleague was held in four different groups, whose winners would then face each other in a playoff to determine the champions, but in 1996 the original league format was restored.

Football, much like most things in Kosovo, had to restart once again and the development of FC Besa Peja was slow as the club began to rebuild from 1999.