Mycotoxins exposure by inhalation and/or dermal contact is possible in different branches of industry especially where heavily dusty settings are present and the handling of dusty commodities is performed. This study aims to explore the validity of the biomonitoring as a tool to investigate the intake of mycotoxins in a population of workers operating in an Italian feed plant. Serum samples were collected for the determination of aflatoxins B1 (AFB1), AFB1-Lysine adduct and ochratoxin A (OTA). A method based on liquid–liquid extraction coupled with high resolution mass spectrometry determination was developed and fully validated. For AFB1, a high number of non-detected samples (90%) was found and no statistical difference was observed comparing workers and control group. None of the analyzed samples showed the presence of AFB1-Lysine adduct. For OTA, the 100% of the analyzed samples was positive with a 33% of the samples showing a concentration higher than the limit of quantification (LOQ), but no statistical difference was highlighted between the average levels of exposed and control groups. In conclusion, the presence of AFB1 and OTA in serum cannot be attributable to occupational exposure.