A study was conducted in the laboratory at ambient temperature of 28±20C and 75±5% relative humidity to evaluate the ability of different packaging materials to maintain qualities of two Nigerian local flours. Harvested yam tuber and cassava root were locally processed into yam flour (Elubo) and cassava flour (Lafun) and was separately packaged with polyethylene, plastic, craft paper and hessian sack. The proximate composition, mineral content, physico-chemical parameters, organoleptic properties, presence of microorganism and insect infestation was recorded after three months of storage. The highest moisture content was recorded in cassava flour stored inside craft paper 15.59 and was significantly (p< 0.05) different from others except cassava flour stored inside hessian sack. The value of acid, peroxide, iodine and FFA was high in flour stored inside craft paper and hessian sack. The physico-chemical properties were higher in cassava flour than the yam flour in different packaging materials. It was noted that the flours stored inside craft paper and hessian sack recorded highest value of microorganism and insect. Therefore, to maintain the quality of yam and cassava flour for long period in storage, plastic and polyethylene bag could be used since they offer better protection than others.