Root-knot nematodes (RKNs) cause huge yield losses to agricultural crops worldwide. Meanwhile, livestock manure is often improperly managed by farmers, which leads to serious environmental pollution. To resolve these two problems, this study developed a procedure for the conversion of chicken manure to organic fertilizer by larvae of Hermetia illucens L. and Bacillus subtilis BSF-CL. Chicken manure organic fertilizer was then mixed thoroughly with Paenibacillus polymyxa KM2501-1 to a final concentration of 1.5×108 CFU g–1. The efficacy of KM2501-1 microbial organic fertilizer in controlling root-knot nematodes was evaluated in pot and field experiments. In pot experiments, applying KM2501-1 microbial organic fertilizer either as a base fertilizer or as a fumigant at the dose of 40 g/pot suppressed root-knot disease by 61.76 and 69.05％ compared to the corresponding control treatments, respectively. When applied as a fumigant at the dose of 1 kg m–2 in field experiments, KM2501-1 microbial organic fertilizer enhanced the growth of tomato plants, suppressed root-knot disease by 49.97％, and reduced second stage juveniles of RKN in soil by 88.68％. KM2501-1 microbial organic fertilizer controlled RKNs better than commercial bio-organic fertilizer in both pot and field experiments. These results demonstrate that this co-conversion process efficiently transforms chicken manure into high value-added larvae biomass and KM2501-1 microbial organic fertilizer with potential application as a novel nematode control agent.