E-waste management is a major environmental concern that also poses serious risks to occupational health. While e-waste workers are exposed to a variety of chemicals, little is known about occupational exposure to microbiological agents. This study aims to fill that gap. For that purpose, two e-waste facilities were assessed: one battery-recycling facility (BRF), and another facility (SRE) dedicated to e-waste sorting and storage before sending it for different processing. Filtering respiratory protection devices (FRPD, 24 samples) and settled dust (13 samples) were collected using standardized sampling approaches, and analyzed by culture-based, chemical and molecular methods. Workers also filled in a questionnaire regarding work activities and the use of FRPD. Microbial contamination, fungal diversity, azole resistance, and prevalence of Aspergillus sections Fumigati and Flavi (as surrogates of harmful fungal contamination) and mycotoxins were determined. To estimate potential health effects related to exposure, the FRPD cytotoxicity was determined in human A549 lung and HepG2 hepatic cells. Microbial contaminants with pathogenicity and toxigenic potential were observed in FRPD and settled dust. Aspergillus section Fumigati was widespread. The observed presence of Aspergillus section Flavi relates to the risk of exposure to aflatoxin B1 (a potent hepatocarcinogen). Four different mycotoxins were detected in 8% FRPD and 15% dust samples, including fumonisin B1 and sterigmatocystin (below the limit of quantification). A low to moderate cytotoxic effect of sampled FRPD was observed, with human lung alveolar cells more sensitive than hepatic cells. No relevant azole resistance was observed, nor correlations between fungal reduced azole-susceptibility and fungal growth at 37 °C or cytotoxicity. In summary, it can be concluded that this approach using FRPD and settled dust presents a promising potential for screening occupational exposure to microbiological contaminants in e-waste management. More studies in this occupational context should be prioritized to identify critical biological hazards and to support the implementation of appropriate health risk mitigation strategies.