Mycotoxins in sesame seeds pose a significant risk to both food safety and Ethiopia’s economy. The purpose of this study was to determine the presence and concentrations of mycotoxins in sesame seeds kept on farms in Ethiopia’s key sesame-producing areas. Purposive sampling was used to obtain 470 sesame seed samples from farmers′ storage facilities in five important districts. Total aflatoxin (AFT), ochratoxin A (OTA), total fumonisin (FUM), and deoxynivalenol (DON) were identified using both a lateral flow reader and an enzyme-linked immunosorbent assay (ELISA). The analysis revealed that all samples contained mycotoxins to varying degrees, with AFT and DON being particularly common. AFT levels varied between 2.5 and 27.8 parts per billion (μg/kg), averaging 13.8 μg/kg, while OTA concentrations were between 5.0 and 9.7 μg/kg, averaging 7.1 μg/kg. Total fumonisin levels spanned from 300 to 1300 μg/kg, averaging 800 μg/kg. DON was found in the range of 560 to 700 μg/kg. Notably, 96.8% of the samples fell within the safe range for AFT, FUM, and DON mean levels as defined by the Federal Drug Administration’s maximum limits. The co-occurrence rates of AFT-OTA, DON-OTA, AFT-FUM, FUM-DON, and FUM-OTA were observed at 44.0%, 38.3%, 33.8%, 30.2%, 29.8%, and 26.0%, respectively. Around 37.2% of the samples showed signs of fungal infection, and seed germination rates varied between 66.8% and 91.1%. The Limmu district exhibited higher total aflatoxin levels, greater kernel infection, and reduced germination rates compared to other districts. The Wollega sesame variety was more susceptible to kernel infection, had higher total aflatoxin levels, and lower germination rates compared to other varieties. Additionally, the age of the grain significantly affected (p < 0.05) both kernel infection and germination. Current storage practices in Ethiopia’s primary sesame-growing districts are conducive to the growth of mycotoxin-producing fungi. Given the public health implications of mycotoxin levels in sesame, it is imperative for stakeholders to collaborate in identifying and implementing secure and effective storage solutions to preserve both the quantity and quality of sesame at the smallholder farmer level. This study underscores the necessity for improved storage technologies to safeguard sesame quality and diminish the risk of mycotoxin contamination.