Sesame is an important oil crop for the Ethiopian economy. However, the lack of adequate storage facilities results in significant losses of sesame seeds. This study was designed to compare the effects of storage conditions and the subsequent impact on sesame seed germination, mold growth, and mycotoxin accumulation over the storage period. The efficacy of two hermetic bags (1. Purdue Improved Crop Storage (PICS) bags and 2. Super GrainPro (SGP) bags) was directly compared to sesame storage in polypropylene (PP bags) and Jute bags. Storage conditions (oxygen, carbon dioxide, temperature, moisture content and relative humidity) of samples were analyzed in the laboratory in three replicates. Results showed that the oxygen concentrations dropped to 6.9% (±0.02) in PICS bags and 8.7% (±0.06) in SGP bags at the end of 6 months of storage. In non-hermetic bags Jute and PP), oxygen levels were close to atmospheric levels at 2-, 4-, and 6-month storage periods. In non-hermetic bags throughout storage, the amount of seed infection by mold constantly increased, and seed germination decreased. Sesame seeds stored in hermetic bags had 89.7% (±0.58) to 88.3% (±2.89) germination rates versus 61.67% (±2.08) for non-hermetic storage bags over the 6-month seed storage period. All mycotoxin levels increased over the same storage period, whereas comparative levels were much lower in hermetic bags after six months. Sesame seeds stored in both hermetic bags had the lowest level of tested mycotoxins, and levels among the SGP and PICS bags were not significantly different from one another. This study provides strong evidence indicating that hermetic storage structures such as PICS and SGP significantly affect temperature, humidity, moisture content, CO2 and oxygen levels resulting in the lowering of fungal growth and mycotoxin accumulation and effectively preserving stored sesame without relying on synthetic pesticides in Ethiopia.