Previous studies anticipated that microorganisms and their metabolites in waste will increase as a consequence of a decreased collection frequency and due to differences in what kind of waste is bagged before collection leading to an increased exposure of workers handling the waste. This study aim was to investigate the microbial contamination present in the waste collection trucks (WCT) and in the support facilities (waste collection station - WCS). It was applied a multi-approach protocol using active (air sampling by impingement and impaction) and passive (surface swabs, electrostatic dust cloths and settled dust) sampling methods. The screening of azole-resistance, the investigation of mycotoxins and the assessment of the elicited biological responses in vitro were also carried out aiming recognizing the possible health effects of waste collection drivers. SARS-CoV-2 detection was also performed. In WCS only air samples had contamination in all the four sampling sites (canteen, operational removal core, operational removal center, and administrative service). Among all the analyzed matrices from the WCT a higher percentage of total bacterial counts and Gram-was detected in swabs (66.93%; 99.36%). In WCS the most common species were Penicillium sp. (43.98%) and Cladosporium sp. (24.68%), while on WCT Aspergillus sp. (4.18%) was also one of the most found. In the azole resistance screening Aspergillus genera was not observed in the azole-supplemented media. SARS-CoV-2 was not detected in any of the environmental samples collected, but Aspergillus section Fumigati was detected in 5 samples. Mycotoxins were not detected in EDC from WCS, while in WCT they were detected in filters (N = 1) and in settled dust samples (N = 16). In conclusion, our study reveals that a comprehensive sampling approach using active and passive sampling (e.g. settled dust sampling for a representative mycotoxin evaluation) and combined analytic methods (i.e., culture-based and molecular) is an important asset in microbial exposure assessments. Concerning the waste collection exposure scenario, the results of this study unveiled a complex exposure, particularly to fungi and their metabolites. Aspergillus section Fumigati highlight the significance of targeting this section in the waste management industry as an indicator of occupational health risk.