Partial cocoa pulp removal may modify substrate availability and affect microbial and metabolic dynamics during fermentation. This study evaluated the effects of beans with pulp and depulped beans on microbial dynamics and metabolite profiles during on-farm cocoa fermentation. Three treatments were evaluated for 144 h: CT, 100% beans with pulp; TA, 75% beans with pulp and 25% depulped beans; and TB, 50% beans with pulp and 50% depulped beans. Physicochemical parameters, culturable microbial populations, selected microbial isolates, sugars, and organic acids were analyzed throughout fermentation. Partial pulp removal was associated with differences in sugar and organic acid profiles, while temperature, pH, and titratable acidity showed the characteristic temporal progression of cocoa fermentation, with significant differences among treatments and fermentation times. Saccharomyces cerevisiae was frequently identified among selected yeast isolates, whereas Acetobacter sp. and Fructobacillus pseudoficulneus were among the bacterial taxa identified. Exploratory principal component and hierarchical cluster analyses indicated that fermentation time was the main factor associated with sample differentiation, while partial pulp removal showed secondary associations with physicochemical and microbiological profiles. Overall, partial pulp removal was associated with differences in microbial and metabolic profiles, indicating its potential for further investigation as a strategy to modulate cocoa fermentation.