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This study was performed to investigate the microbiological contamination of digestate product (DP) obtained from the anaerobic co-digestion of bovine manure and agricultural by-products.Microbiological analyses were performed on bovine manure, fresh DP, liquid and solid fractions and stored liquid fraction of DP. A statistically significant reduction of faecal bacterial indicator was found after anaerobic digestion except for enterococci. After liquid/solid DP separation, bacteria tend to be concentrated in the solid fraction. Storage does not seem to influence the indicator parameters, except for enterococci. Escherichia coli O157:H7 and Yersinia were not found in any samples analysed. Salmonella was rarely detected in DP samples and its derivates, while Listeria monocytogenes was encountered in many samples.The results obtained indicate that the hygienic quality of DP is for almost all microbiological parameters better than that of the bovine manure (range of reduction 1.6–3.1 log10) and suggest the need to identify specific pathogen indicators related to the hygienic characteristics of DPs.This study highlights that the anaerobic co-digestion of bovine manure and agricultural by-products in a field-scale biogas plant does not increase human health risk with respect to the use of animal manure for agricultural fertilization.