Sesame seeds serve as a crucial source of sustenance, nutrition, and economic value in developing nations. Ensuring optimal storage conditions is vital for mitigating the risk of mycotoxin contamination. This study employed regression analysis on historical data to assess the impact of storage environmental conditions on fungal growth and mycotoxin generation in sesame, aiming to enhance the storage practices of smallholder farmers. This research utilized both linear and non-linear regression models to investigate how various environmental factors, including temperature, humidity, moisture content, and gas levels, influence the proliferation of fungi and the production of mycotoxins in sesame seeds during storage. The findings indicate that keeping seed moisture content under 6% and the temperature inside the storage below 20°C effectively reduces aflatoxin levels in hermetically sealed bags. Conversely, in traditional bags, aflatoxin levels tend to rise, primarily due to increased seed moisture. This study also discovered a significant correlation between the rise of Ochratoxin A levels and the presence of Penicillium and Aspergillus infections in sesame seeds. Notably, Ochratoxin A levels were below 6 ppb when there was a 50% combination of Penicillium and Aspergillus. This suggests that these fungi play a substantial role in generating Ochratoxin A in stored sesame. Effective management of mycotoxins in stored sesame can be achieved through careful control of abiotic factors, highlighting the crucial role of storage environment in preventing fungal contamination and mycotoxin production.