Environmentally sustainable methods of waste disposal are a strategic priority. For organic waste management and innovative biological treatments present advantageous opportunities, although organic waste treatment also includes environmental drawbacks, such as bioaerosol pro-duction. This study aims to evaluate bioaerosol spread during an innovative experimental treatment. The process consists of two anaerobic steps: acidogenesis, which includes polyhydroxyalkanoate accumulation, followed by methanogenesis. Bioaerosol, PM10, and endotoxin concentrations were measured at three sampling points during different campaigns to evaluate: (1) the background levels, (2) the contamination produced in the pre-treatment stage, and (3) the residual contamination of the outgoing digested sludge. Environmental PM10 seemed to be generally quite contained, while the endotoxin determination was close to 90 EU/m3. Significant microbial concentrations were detected during the loading of the organic fraction of municipal solid waste (fungi > 1300 CFU/m3, Bacillus genus (≈103 CFU/m3), higher Clostridium spp. and opportunistic human pathogens such as Pseudomonas aeruginosa and Klebsiella pneumoniae), suggesting a significant contamination level. Such results are useful for hazard identification in the risk assessment of innovative processes, as they reveal contaminants potentially harmful to both workers’ health and the environment