Abstract Reductive soil disinfestation (RSD) and chemical soil disinfestation (CSD) are two common agricultural strategies for the elimination of soil-borne pathogens. However, the differences in soil bacterial microbiome and its associated functional characteristics between CSD and RSD are poorly understood. In this study, five soil treatments, un-treated control (CK), CSD with 0.5 t ha−1 dazomet (DZ), RSD with 10 t ha−1 ethanol (ET), 15 t ha−1 sugarcane bagasse (SB), and 15 t ha−1 bean dregs (BD), were compared. We evaluated their effects on microbial metabolic activity, functional diversity, nitrogen-related genes abundance, and bacterial community structure using Biolog analysis, real-time PCR, and high-throughput sequencing. RSD-related treatments improved soil metabolic activity, functional diversity, and the abundance of denitrifying genes to a greater extent than the DZ treatment. Carbon source utilization preference and bacterial community structure were strikingly altered by CSD and RSD practices. Bacterial richness, diversity, and evenness were notably lowered in the SB- and BD-treated soils compared with the CK and DZ-treated soils. Moreover, compared with the DZ- and ET-treated soils, the SB- and BD-treated soils harbored distinct unique and core microbiomes that were comprised of more abundant and diverse potentially disease-suppressive and organic-decomposable agents. Collectively, these results suggest that RSD practices incorporated with organic residues could considerably restore soil functional activity and diversity, and act as a potential agricultural practice for the development of disease-suppressive soils.