Black soldier fly larvae (BSFL) are widely used in recycling and upcycling of nutrients in agri-food by-products, but low and inconsistent BSFL rearing performance (i.e. larval growth, bioconversion rate, and substrate reduction) has been identified as a key challenge. The aims of this research were two-fold: (1) validate an existing closed rearing system design; and (2) assess whether a microbial inoculum derived from the rearing residue increases rearing performance. In controlled bench-scale experiments, BSFL were reared on tomato pomace (TP) and white wine pomace (WWP), along with food waste as control substrate. The two aims were assessed based on the following response variables: larval mass, substrate reduction, residue properties (i.e. pH, temperature, moisture content), and larval intestinal and residue microbiota. Higher BSFL mass (by 5.1 mg dry mass) at harvest on WWP and substrate reduction on TP (by 11.7% dry mass) in the closed system compared to the open system confirmed the potential of closed systems for rearing performance improvements of agri-food by-products. The rearing system also affected the residual moisture content and temperature, but only had a small effect on microbiota. Performance improvements by the closed rearing system design may be outweighed by insufficient aeration with pasty substrates and higher operational efforts for aeration and larval separation from the high-moisture residues. In contrast to the rearing system design, addition of the residue-derived microbial inoculum did not result in improved performance, nor did it alter intestinal and residue microbiota. Missing performance improvements could have been due to absent or low numbers of probiotic bacteria. The success of microbial substrate supplementation could be improved by studying effects of larval-associated microbes and developing cultivation methods that selectively amplify the beneficial (yet unknown) members of the microbial community. Our investigations aimed to increase the valorisation of low-value agri-food by-products in BSFL rearing.