In sub-Saharan Africa, there is a high demand for affordable and accessible methods for on-site detection of aflatoxins for appropriate food safety management. In this study, we validated an electrochemical immunosensor device by the on-site detection of 60 maize flour samples from six markets and 72 samples from households in Kampala. The immunosensor was successfully validated with a linear range from 0.7 ± 0.1 to 11 ± 0.3 µg/kg and limit of detection (LOD) of 0.7 µg/kg. The maize flour samples from the markets had a mean total aflatoxin concentration of 7.6 ± 2.3 µg/kg with approximately 20% of the samples higher than 10 µg/kg, which is the maximum acceptable level in East Africa. Further down the distribution chain, at the household level, approximately 45% of the total number contained total aflatoxin levels higher than the acceptable limit. The on-site detection method correlated well with the established laboratory-based HPLC and ELISA-detection methods for aflatoxin B1 with the correlation coefficients of 0.94 and 0.98, respectively. This study shows the feasibility of a novel on-site detection method and articulates the severity of aflatoxin contamination in Uganda.