This paper investigated the effects of agroforestry (AF) on the sensory profiles of cocoa beans and the organoleptic quality of end-chocolates. A three-day opening delay for the Ivorian hybrid cultivar commonly known as “Mercedes” (Amelonado × West African Trinitario) from AF and full-sun (FS) plantations as control located at five cocoa-producing areas were fermented in wooden boxes for 6 days and stirred at days 2 and 4. Fermented cocoa was sun-dried until reaching 7–8% moisture and processed into chocolate. Volatile compounds of cocoa powder and chocolate were analyzed using the SPME-GC-MS method, while the organoleptic perception of chocolates was assessed by 12 professional judges according to 10 sensory descriptors. The findings revealed that the concentrations of esters ranged from 9.41 ± 0.61 to 19.35 ± 1.28 µg.g-1, aldehydes from 11.56 ± 0.7 to 25.33 ± 1.5 µg.g-1, and ketones from 5.76 ± 0.62 to 55.84 ± 4.39 µg.g-1 in cocoa beans regardless of the cropping system. However, the concentrations of some volatile compounds classes including alcohols, acids, and pyrazines were similar in AF and FS chocolate samples. AF system clearly influenced the volatile compound profiles of cocoa beans in only the Adzopé, Guibéroua, and Méagui regions without impacting those of the chocolates regardless of the geographical origin after fermentation and roasting. Furthermore, AF chocolate was not less appealing than the FS chocolate samples. So, AF system did not significantly influence the sensory perception of chocolate. AF can therefore be encouraged as a cropping system for cocoa cultivation to reduce deforestation and promote reforestation, ensuring the sustainability of cocoa.