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The 2016 CFA Integration Championship was the 31st season of the CFA Integration Championship. Atlas Aglandjias clinched their 1st CFA Integration Championship trophy after a 2–1 victory over Anagennisi Trachoniou.

Format
Twenty two teams from local federations members of the Confederation of local federations of Cyprus (STOK) participated in the 2016 CFA Integration Championship.

The competition consisted of five knock-out rounds. In all rounds each tie was played as a single leg and was held at a neutral stadium. Each tie winner qualified to the next round. If a match was drawn, extra time was following. If extra time was also drawn, the winner was decided by penalty shoot-out.

The four teams that qualified to semiifinals were promoted to the 2016–17 STOK Elite Division.

Participating teams
Different number of teams from each local federation participated in the STOK Integration Championship. Those teams were the champions and the first teams of each local federation championship. Participation was not compulsory. The table below list the participating teams and their local federation.

(C.) : Champions of local federation

First round
In the first round 12 of 22 teams were participated. The 9 champions advanced directly to the second round and met the winners of the first round ties. Elia Lythrodonta advanced directly to the second round, without playing any match.

Second round
In the second round participated all the teams that were qualified from the first round and the six teams that were excluded from the first round.

Quarter-finals
The 8 teams that were qualified from the second round were participated.

Semifinals
The 8 teams that were qualified from the quarterfinals round were participated.