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Anaerobic digestion is an emerging technology producing energy from renewable resources or food waste. Exposure screenings, comprising hazardous substances and biological agents, at different workplaces are necessary for a comprehensive overview of potential hazards in order to assess the risk of employees in biogas plants. In order to analyse these parameters, workplace measurements were conducted in seven full-scale anaerobic digesters. Personal and stationary sampling was performed for inhalable and respirable particles, volatile organic compounds, ammonia, hydrogen sulphide, carbon monoxide, and carbon dioxide. Furthermore, concentrations of the total cell count, endotoxins, and fungi—down to species level—were determined in comparison to windward air. Sequencing of the 16S rRNA genes was utilized for the determination of the bacterial composition inside the biogas plants. Measurements of hazardous substances show hardly values reaching the specific occupational exposure limit value, except ammonia. An approximate 5-fold increase in the median of the total cell count, 15-fold in endotoxins, and 4-fold in fungi was monitored in the biogas plants compared with windward air. Specifying the comparison to selected workplaces showed the highest concentrations of these parameters for workplaces related to delivery and cleaning. Strikingly, the fungal composition drastically changed between windward air and burdened workplaces with an increase of Aspergillusspecies up to 250-fold and Penicilliumspecies up to 400-fold. Sequence analyses of 16S rRNA genes revealed that many workplaces are dominated by the order of Bacillales or Lactobacillales, but many sequences were not assignable to known bacteria. Although significant changes inside the biogas plant compared with windward air were identified, that increase does not suggest stricter occupational safety measures at least when applying German policies. However, exposure to biological agents revealed wide ranges and specific workplace measurements should be conducted for risk assessment.