A major barrier for using animal waste as substrate for production of insects for feed or food is the concern for safety of the end products. In this study we investigated how rearing of fly larvae of Musca domestica in poultry manure influenced the counts of three pathogenic test strains (Escherichia coli, Salmonella Enteritidis and Campylobacter jejuni) and investigated whether these were transferred from manure to larvae, pupae or adults flies. We monitored quantitative microbiological changes over a study period of seven days. We showed that the decay in the numbers of E. coli, S. Enteritidis, and C. jejuni was faster in manure with rearing of fly larvae than in manure without larvae; an 8 log10 reduction of all three test bacteria was observed within four days in manure with larvae; compared to manure without larvae where a 1 to 2 log10 was observed. We found no sign of propagation of the pathogens in the larvae gut. All test strains were detectable in low numbers at day 4 in the larvae gut but only C. jejuni survived until day 7. In the pupae, only S. Enteritidis was detectable at day 3, and no test strains were found later than day 3. None of the test strain was isolated from adult flies. The total aerobic bacterial count remained at a high level throughout the study both in manure, in larvae and in pupae. In conclusion, our results showed that elimination of the pathogens from the manure was accelerated by larvae rearing, but were still detectable at low number in the larvae gut until end of the larvae stage. This study provides data for evaluation of feed safety of fly larvae reared on animal waste. Furthermore suggests a potential use for reduction of these pathogens in manure.