Published in Science Direct. Due to higher microbial activity and diversity, organic farming serves as a sustainable alternative in preventing several soil-borne plant diseases. However, there are limited studies that have shown direct relationship between soil bacterial composition and its effect on disease suppressive potential under different farming systems. Thus, the objective of the study was to understand the effect of farming practices on disease suppressive ability of the soil using a long-term (managed since 18 years) field experiment under organic and conventional farming management. Amplicon sequencing revealed higher abundance of several biocontrol genera in organic field compared to conventional field. The diversity indices for bacterial communities were significantly higher in soil from organic field. Subsequently, the comparative disease suppressive potential of the two management practices was validated in planta against two model phytopathogens, Rhizoctonia solani and Fusarium oxysporum. The disease severity was less in plants treated with microbiome from organic field compared to that of conventional field. The study revealed the key taxa such as Flavobacterium, Bacillus, Pseudomonas, Planctomycetes etc. with potential to impart disease suppressiveness in organic field. This can serve as the basis for generation of synthetic microbial community to induce suppressiveness in otherwise conducive soil.