AbstractBACKGROUNDBlack soldier fly larvae (BSFL) offer very good prospects for the production of cheap and high‐quality dietary protein. This insect is able to consume low‐quality substrates, including food waste. The properties and safety of the compost obtained are largely determined by its microbiome. However, while the bacterial component of the BSFL‐compost microbiome has been much studied, little is known about its fungal component. In plant‐based rearing substrates both the biomass and the metabolic activity of fungi often exceed the biomass and the activity of prokaryotes. So, the purpose of this study was to investigate the fungal community of the compost produced by BSF larvae reared on a food waste substrate.RESULTSCommunity structure was determined by metabarcoding of the ITS (internal transcribed spacer) region. Species composition and abundance were determined using the plating technique and subsequent identification of the isolated pure cultures. It was found that the primary mycobiome of the food waste substrate that was used consisted of 19 families, represented mainly by phytopathogenic and endophytic genera. Larva incubation led to the complete elimination of all mycelial fungi from the resulting compost. The final mycobiome consisted of only two yeast species, Pichia kudriavzevii and Diutina rugosa, with a total abundance of 1.2 × 107 CFU g−1.CONCLUSIONSThe rearing of BSFL led to the complete elimination of mycelial fungi from its feed substrate. The final compost lacked harmful fungi, including molds. This information may be crucial for BSF compost utilization. The phenomenon was also an interesting aspect of zoomicrobial interactions in nature and agriculture. © 2021 Society of Chemical Industry.