A study was conducted using maize samples collected from different agroecological zones of Kenya (n = 471) and Tanzania (n = 100) during the 2013 maize harvest season to estimate a relationship between aflatoxin B1 concentration and occurrence with weather conditions during the growing season. The toxins were analysed by the ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. Aflatoxin B1 incidence ranged between 0–100% of samples in different regions with an average value of 29.4% and aflatoxin concentrations of up to 6075 µg/kg recorded in one sample. Several regression techniques were explored. Random forests achieved the highest overall accuracy of 80%, while the accuracy of a logistic regression model was 65%. Low rainfall occurring during the early stage of the maize plant maturing combined with high temperatures leading up to full maturity provide warning signs of aflatoxin contamination. Risk maps for the two countries for the 2013 season were generated using both random forests and logistic regression models.