Consumption of maize and maize-based products contributes a significant percentage to the total food energy intake in Uganda. However, the production of maize-derived foodstuffs is performed traditionally or by small- and medium-scale processors using different processing techniques. This can lead to differences in the quality of these products from processors, raising food safety concerns. In this study, the effects of mechanical processing (milling) methods on deposition of heavy metals into milled maize flour and the associated consumption health risks were assessed. Atomic absorption spectrophotometry was used to quantitatively establish the concentration of iron (Fe), manganese (Mn), zinc (Zn), cadmium (Cd), lead (Pb), chromium (Cr), copper (Cu), cobalt (Co) and nickel (Ni) in 100 samples of maize milled using a wooden mortar (n = 2), a metallic mortar (n = 2), diesel engine-powered mills (n = 48) and electric motor-powered mills (n = 48). Results showed that the mean concentrations of heavy metals in mg/kg were Fe (11.60-34.45), Cu (0.50-8.10), Ni (0.50-1.60), Mn (0.70-25.40), Zn (4.40-15.90), Pb (0.53-10.20), Cd (0.51-0.85), Cr (0.50-1.53) and Co (0.50-1.51). The highest concentrations were found in flour milled using a traditional metallic mortar while the lowest levels were in those samples milled using a wooden mortar. The Fe, Pb and Cd contents of flours produced using the metallic mortar and some commercial mills was found to be higher than the permissible limits set by WHO/FAO. Human health risk assessment showed that there are potential carcinogenic health risks from adults' intake of heavy metals in maize flour milled using a metallic mortar. Therefore, processing of maize flour needs to be monitored by the relevant statutory bodies in Uganda to minimize the possibility of heavy metal contamination of food products and animal feeds.