Little attention has been paid to on-farm cocoa fermentation practices, leading to poor-quality cocoa beans. A cross-sectional study was conducted in three agroecological zones of Uganda (Lake Victoria Crescent, Western Rangelands, and Lake Albert Crescent) to investigate on-farm fermentation practices, the association between farmer training and adoption of recommended fermentation practices as well as the impact of fermentation practices on cocoa quality. Data on fermentation practices and farmer training was collected using a questionnaire. The quality of cocoa beans collected from interviewed farmers was assessed for bean cut test, fermentation index, pH, and titratable acidity following recommended methods. Results revealed significant variation in fermentation practices used by farmers, with over 65% employing rudimentary methods such as sack, bucket, and jerrycan. Training of farmers did not increase the likelihood of farmers adopting the recommended fermentation practices. As a result, the quality of fermented cocoa beans was low with only 40-51% of the beans from all zones exhibiting the fully brown color, which is below the 60% threshold for commercial-grade cocoa beans. Furthermore, the fermentation index of cocoa beans from all zones ranged from 0.61-0.67, indicating a high percentage of under-fermented beans. Farmers who used the recommended practices (heap and box fermentation for 5-7 days while turning cocoa) in each zone, produced cocoa with a significantly (p<0.05) higher percentage of fully fermented beans. The continued use of rudimentary postharvest handling practices among farmers leads to the production of poor-quality cocoa beans. It is important to strengthen the enforcement of recommended fermentation practices to improve the quality of cocoa beans and ensure a sustainable market.