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The plant–parasitic Root Knot Nematodes (Meloidogynespp.,) play a pivotal role to devastate vegetable crops across the globe. Considering the significance of plant–microbe interaction in the suppression of Root Knot Nematode, we investigated the diversity of microbiome associated with bioagents-treated and nematode-infected rhizosphere soil samples through metagenomics approach. The wide variety of organisms spread across different ecosystems showed the highest average abundance within each taxonomic level. In the rhizosphere, Proteobacteria, Firmicutes, and Actinobacteria were the dominant bacterial taxa, while Ascomycota, Basidiomycota, and Mucoromycota were prevalent among the fungal taxa. Regardless of the specific treatments, bacterial genera like Bacillus, Sphingomonas, and Pseudomonaswere consistently found in high abundance. Shannon diversity index vividly ensured that, bacterial communities were maximum in B. velezensisVB7-treated soil (1.4–2.4), followed by Root Knot Nematode-associated soils (1.3–2.2), whereas richness was higher with Trichoderma konigiopsisTK drenched soils (1.3–2.0). The predominant occurrence of fungal genera such as Aspergillus Epicoccum, Choanephora, Alternariaand Thanatephorushabituate rhizosphere soils. Shannon index expressed the abundant richness of fungal species in treated samples (1.04–0.90). Further, refraction and species diversity curve also depicted a significant increase with maximum diversity of fungal species in B. velezensisVB7-treated soil than T. koningiopsisand nematode-infested soil. In field trial, bioagents-treated tomato plant (60% reduction of Meloidogyne incognitainfection) had reduced gall index along with enhanced plant growth and increased fruit yield in comparison with the untreated plant. Hence, B. velezensisVB7 and T. koingiopsiscan be well explored as an antinemic bioagents against RKN.