Recommended cassava roots’ storage methods of trench and moist sawdust were investigated for their effects on moisture contents and microbial quality of cassava roots under cooling sheds. The storage methods’ shed temperatures and relative humidity were respectively similar and steady at about 24°C temperature and about 80% relative humidity. Moisture contents of the freshly harvested ‘Bitter’ and “Sweet” cassava roots were 57.7% and 59.9% respectively. The freshly harvested roots were uninfected, but showed various bacteria and fungi growths during storage. The bacteria and fungi species isolated from samples of stored cassava roots depended on storage method and cassava variety. The highest total bacterial load (6.48 x 105 cfu/g) and highest total fungal load (3.0 x 105 cfu/g) were within allowable load limits (107 cfu/g) for fresh cassava. Moisture content reduction in cassava roots was higher in trench than in moist sawdust. However, moisture content reductions in cassava roots of about 4% in trench and 3% in moist sawdust were considered low in the 6 weeks storage trial. However, microbial contamination and growths on stored cassava roots called for aseptic diligence in use of the potentially beneficial storage methods.