Anaerobic digestion is a consolidated biotechnology able to produce renewable energy from biomasses. In the European countries, quick growth of biogas production from different organic matrices including wastes has been observed. In relation to the characteristics and quantity of the anaerobic digestion of feedstock, there are different technologies, advantages and criticisms. An accurate occupational risk assessment and development of management tools for green jobs involved in the anaerobic digestion plants are due. The aim of this work is to assess the aerosol exposure for such workers, focusing on the bioaerosol risk. Full scale plants for the treatment of organic municipal waste, waste water treatment sludge, agro zootechnical and food producing byproducts were involved for this purpose. The bioaerosol levels were monitored during activities through culturing and biomolecular methods; moreover, the sub-fractionated PM10 and carried endotoxins were measured in different plant areas. Global microbial contamination is higher (>5000 UFC/m3) in the area where organic wastes are handled and pretreated, both for organic municipal waste plants - with a bacterial prevalence - and agro zootechnical plants - with a fungi prevalence. Moreover, the microbial contamination is higher where organic municipal waste is present in respect to other biomasses (ANOVA p < 0.01). Numerous pathogens are carried by the aerosol. HAdV-4 presence is lower than LOQ (50 gene copies/m3) in all the samples. Environmental PM10 reached the 280 µg/m3 level including PM3 for 78%. Endotoxin pollution overtakes the 90 EU/m3 limit sporadically. Personal PM4.5 reached 10 mg/m3 only for maintenance technicians in the pretreatment area for organic municipal waste. The risk can be evaluated under a quantitative and qualitative point of view highlighting risk management improvement for anaerobic digestion plants.