Cyanobacteria, as organic matter with a high protein content, have great potential as feed additives, and the use of black soldier fly larvae (BSFL) to convert organic waste into biomass that is rich in protein and fat is a proven process. Accordingly, the study evaluated the beneficial effects of microbial inoculation (Bacillus subtilis, yeast, Lactobacillus plantarum, and a mixture of those three microorganisms) on the growth performance, and nutrient accumulation of BSFL based on utilizing cyanobacteria as feedstock. The mixed microorganism addition group showed the most significant increase in the BSFL biotransformation efficiency compared to the control group, with a 16.73% increase in larvae weight, a 9.33% increase in dry matter reduction rate, a 16.90% increase in bioconversion rate, and also a reduction in developmental time. The amino acid content of all microorganism-added groups was increased, bring the larvae amino acid composition closer to that of soybean meal. Furthermore, microbial addition also resulted in a significant enrichment in larvae lauric acid (> 40%) and a decrease (< 33%) in unsaturated fatty acid. Microbial addition altered the structure of the larvae gut microbial community, resulting in an increase and a decrease in the abundances of Actinobacteria and Proteobacteria, respectively. Metabolomic analyses demonstrated that the addition of microorganisms improved the ability of larvae to utilize nutrients and increased the accumulation of short-chain fatty acid metabolites. The study advances a new approach to the utilization of cyanobacteria and provides guidance for establishing an efficient process for the conversion of organic solid waste by BSFL.