Plastic plug-flow bio-digesters have been promoted as a good option for improved treatment of manure and wastewater in developing countries although minimal information has been published on their hygienic status. This bench-scale study replicates bio-digester conditions to evaluate the reduction of pathogen and indicator microorganisms at three different hydraulic retention times (HRT) in the anaerobic treatment of pig manures at 30°C for 50 days. Results showed that physicochemical values differed between HRTs. Gas production efficiency was better for longer HRTs. The accumulated sludge at the reactor's base increased with longer HRT. Phages and bacteria examined were reduced, but none was completely eliminated. Log10 reduction of bacteria ranged from 0.54 to 2.47. Phages ranged from 1.60 to 3.42. The reduction of organisms at HRT = 30 days was about one log10 unit higher than HRT = 15 days and about two log10 units higher than HRT = 3 days. The results indicate that the reduction of tested organisms increases with HRT. However the hygienic quality of the liquid effluent does not meet required quality values for surface and irrigation water. Longer HRTs are recommended to increase gas yield and achieve higher pathogen reduction. More barriers should be applied while handling bio-digester outputs to minimise risks to environmental and human health.