In the context of climate change and depletion of natural resources, meeting the growing demand for animal feed and human food through sufficient, nutritious, safe, and affordable sources of protein is becoming a priority. The use of Hermetia illucens, the black soldier fly (BSF), has emerged as a strategy to enhance the circularity of the agri-food chain, but its microbiological safety remains a concern. The aim of the present study was to systematically review available data on the microbiological quality of BSF and to investigate the impact of using four different rearing substrates including classic options allowed by the EU regulation (cereals, fruits, vegetables) and options not allowed by EU regulations regarding vegetable agri-food (co-products, food at shelf life, and meat). A total of 13 studies were collected and synthesized, including 910 sample results, while 102 new sample results were collected from the present experiments in three farms. Both datasets combined revealed a high level of contamination of larvae, potentially transmitted through the substrate. The main pathogenic bacteria identified were Bacillus cereus, Clostridium perfringens, Cronobacter spp., Escherichia coli, Salmonella spp., and Staphylococcus aureus coagulase-positive, while Campylobacter spp. and Listeria monocytogenes were not detected. Any of these four substrates were excluded for their use in insect rearing; however, safety concerns were confirmed and must be managed by the operators of the sector using microbial inactivation treatment after the harvest of the larvae in order to propose safe products for the market. The results obtained will guide the definition of the control criteria and optimize the following manufacturing steps.