1JS Saint-Pierroise withdrew due to high travel costs; they were banned from AFC competitions for three years and fined $3500. 2Sporting Clube da Praia refused to travel due to civil unrest and a violent general strike in Guinea. 3Super ESCOM withdrew. 4AS Douanes were ejected from the competition for fielding an ineligible player. 5 The tie was played over one leg because AGSM did not have an international-standard ground.
First round
1st legs were played on 2–4 March 2007.
2nd legs were played on 16–18 March 2007.
1The match was abandoned in the 82nd minute with Maranatha leading 2-0 after APR FC walked off protesting a penalty award against them; APR FC were ejected from the competition and banned from CAF competitions for three years.
Second round
1st legs were played on 6–8 April 2007.
2nd legs were played on 20–22 April 2007.