In certain location, it is undeniable that there are qualities variations of fermented cocoa beans depend on processing techniques. In addition, its cocoa bean's production central at Yogyakarta have their specific characteristic own regarding the use of fermentation box (box type). The purpose of this research was to analyze the effects of three types of fermentation box and duration to fungi level of fermented cocoa beans. CRD (completely randomized design) with two factors and three replications is applied as assessment method. The first factor is the type of fermentation box (basket, storey box and single box with a hand crank) and the second factor is the length of fermentation time (3 and 5 days). The result of the research explained that the lowest levels of the fungi achieve within 5 days of fermentation processes. Meanwhile, a single box with a hand crank provide the lowest of fungi's level. Furthermore, the combination of those two results may give the most favorably expected condition of fungi level.