This study determined the influence of selected yeast starters on the antioxidant content, volatile organic compounds and sensory qualities of fermented cocoa beans. Cocoa beans fermented with Hanseniaspora thailandica (MH979675), Pichia kudriazevii (MH979681), or a mixture of both species in fermentation (20 kg) were highly reproducible based on the physicochemical parameters (temperature, pH of nibs, fermentation index and cut test). The usage of H. thailandica improved the total polyphenols content of cocoa beans with fermentation index around 1.24 and 1.33. The correlation analyses suggested that phenolics and flavonoids compounds may not be the main constituents that led to the antioxidant activities of the fermented samples. Principal Component Analysis showed distinct differences in VOC profiles between spontaneous and fermentation using yeast. Sweet and spicy notes were only found in sample fermented with yeast. The inoculation of yeast in fermentation influenced the sensorial and antioxidant properties of cocoa beans.