The conventional method of grain storage involving the use of polypropylene bags in conjunction with pesticides and hermetic bags are paramount in developing countries. However, there is limited information on grain quality and pesticide residue concentration of maize stored in such bags. This work determined grain quality and pesticide residue concentrations of maize stored in polypropylene and hermetic storage bags. Maize samples stored for a period of one year in polypropylene and hermetic bags were obtained from three major maize growing communities in the Ashanti region of Ghana and were analyzed for grain quality, aflatoxin content and pesticide residue concentration using standard methods. The amount of diseased, discolored, broken, insect-damaged, stained, germinated, shriveled, total defective, inorganic and organic matter of maize stored in hermetic bags was significantly lower than that of polypropylene. Levels of aflatoxin in maize stored in the polypropylene bags were significantly higher (13.9 ppb–20 ppb) than in maize stored in the hermetic bags (0.90 ppb–2.6 ppb). Out of 35 pesticides screened, only lambda-cyhalothrin was detected in polypropylene bags and deltamethrin in hermetic bags. The presence of these pesticide residues may be due to their long-lasting abilities. Levels of lambda-cyhalothrin residues were above the maximum residue limit (MRL) of 0.02 mg/kg, but have no significant effect on health. Deltamethrin residue concentrations in hermetically stored maize samples were below the MRL. In conclusion, maize grains stored in hermetic bags have higher grain quality and lower aflatoxin and pesticide residue concentrations than polypropylene bags. Education and promotion on the utilization of hermetic bags should be a priority in storing and supplying safe maize grains to consumers.