Black soldier fly, Hermetia illucens (L.) (Diptera: Stratiomyidae) can be used for recycling a wide variety of organic wastes. However, these wastes are also suitable for colonisation by pest fly species, including the blow fly Lucilia sericata (Meigen) (Diptera: Calliphoridae), and by pathogenic microorganisms. We tested effects of the presence of black soldier fly larvae (BSFL) on recruitment and retention of blow fly larvae, as well as on composition and dynamics of microbial communities in finfish-based substrates. Substrates inhabited by BSFL contained approximately one-tenth of the L. sericata pupae found in the control substrate even when BSFL were removed prior to the introduction of gravid L. sericata females. Furthermore, almost three-quarters of L. sericata released into substrates previously colonised by BSFL emigrated within 24 h, while no such emigration was detected for the control substrates. Unlike previous studies, bacterial community was heavily dominated by Gram-positive species. Overall bacterial abundance on BSFL substrates declined approximately two-fold compared to the control substrate, while fungal abundance increased. However, surviving microbial communities were still robust and diverse, and continued to be dominated by Gram-positive bacteria. On the other hand, Gram-negative Shigella sonnei, which is a common cause of diarrhoea in humans, was more than 200 times less abundant in BSFL substrates compared to the control throughout the experiment. Repellent and antibiotic properties observed in this study are advantageous for using BSFL in remediation of finfish wastes. However, additional treatment of remaining residue may still be necessary to eliminate all biological contamination.