Purpose: Organic farming practices enhance soil health by the addition of bio-amendments, which improve microbial diversity and abundance. Improved soil health, due to enhanced dynamic interactions between abiotic and biotic components of the environment, impedes the progression of diseases caused by soil-borne phytopathogens. The present study aimed to characterize the critical microbial and edaphic factors in correlation with phytopathogen suppression in soil from mustard fields managed under different farming practices. Methods and results: Organic soil exhibited better suppression of phytopathogens, availability of macronutrients, and high biocontrol enzymatic activities than soil from conventionally managed field. In terms of maximal phytopathogen suppression, Fusarium solani was suppressed to 85% by fungal fraction of organic soil, whereas F. fujikori was suppressed to 77% by bacterial fraction of organic soil. However, available micronutrients were higher in conventionally managed soils. Positive correlations between enhanced biocontrol enzyme activities and organic farming practice were deciphered, highlighting improved disease suppressive potential of organic soil. Metagenomic sequencing of the rhizosphere soil from mustard plants grown using “Jeevan Jyoti” bio-amendment and conventional farming regimes revealed that microbial communities could play key roles in modulating general disease suppressiveness of soil. Functional annotation enabled the identification of dominant biological processes, impacting plant and soil health positively. Specifically, the open reading frames coding for bacterial proteins involved in transport and key cellular processes were enriched in datasets of organic farm soil. Conclusion: The evidences from this study delineate the correlation between microbial components present in rhizosphere soil and edaphic factors, in the context of general disease suppressiveness.