During the last decade, edible insects have successfully taken a meaningful position in the feed and food chain. To expand this position, product safety continuously needs to be warranted. This review focuses on the current knowledge and the future challenges on the prevalence of human foodborne pathogens in edible insects. The top three of the bacterial pathogens associated with insects for food are Staphylococcus aureus, pathogenic Clostridium spp. and pathogenic species of the Bacillus cereus group. Less is known about other types of biological contaminants, the fungi, viruses, protozoa and prions. For insects for feed, even less reports on pathogens are available so far, although the microbiota of Hermetia illucens is increasingly being studied in the latest years. In addition to the evaluation of endogenous microorganisms in insects, an overview is given of inoculation experiments to study the fate of specific food pathogens during rearing. Future challenges that are identified mainly relate to the fact that risk assessments directed to specific insect species are needed. Also, more research data are needed on the microbiological quality of substrates and residue, in connection with decontamination treatments. The house flora of rearing facilities has not been investigated before. The insect supply chain can generate insights in the microbiological quality of the integral chain by implementing exhaustive sampling plans and by applying predictive microbiology. Additionally, microbiological methods used in research and quality control require standardisation. Rather unexplored so far is the unculturable fraction of the insect microbial community and its importance in food safety. Last but not least, the most important microbiological challenge may well be situated in the further development of the sector: upscaling in terms of capacity and number of companies will increase the complexity of the sector. That will have implications for monitoring and control of biological contaminants.