Following the decision of the Maltese Football Association Executive Committee, the teams that had finished in the promotion and relegation places in the previous Challenge League season would remain in the Challenge League in the 2021-22 season (with the exception of Qormi, due to less than 75% of the matches having been completed in the competition.
This season therefore saw twenty-two teams competed rather than the sixteen that had been originally expected.
[4][5] The six teams to finish in the bottom three places of both groups relegated to the National Amateur League the following season.
The top two teams from either group achieved automatic promotion with the end of season leaders of the two groups meeting in a playoff to decide who will be the champion for 2021-22.
The bottom three clubs of both groups automatically relegated without any playoffs.