In this study, the interaction of biosynthesized silver nanoparticles (BSNP) with native soil via plant transport was assessed in model pathosystem of Arabidopsis thaliana and Alternaria brassicicola. Foliar application of 5μg/mL of BSNP reduced number of spores of fungi to 2.2×105 from 7×105, while numbers of lesions got reduced to 0.9/leaf in treated plants compared to 2.9/leaf in pathogen-infected plant without altering soil pH, electric conductivity, soil organic carbon and soil microbial biomass carbon. Soil enzyme activities including dehydrogenase, acid and alkaline phosphatase, urease, β-glucosidase and protease did not alter significantly in BSNP-treated plants compared to control plants. Application of BSNP did not alter the number of cultivable bacteria, fungi and actinomycetes. Effect of BSNP on uncultured bacterial diversity was measured by DGGE analysis which revealed similar banding pattern in all different treatments except in A. brassicicola-infected (AB) and A. brassicicola-infected plants treated with silver nanoparticles (AB+BSNP) after 120days. Although AB-infected plants exhibited a decrease in bacterial diversity, treatment of AB+BSNP after 120days demonstrated maximum bacterial diversity. McIntosh, Shannon, and Simpson diversity indices were calculated based on carbon source utilization pattern by BIOLOG analysis, revealing no significant difference among all treatments in different time intervals. BSNPs have the potential to act as strong antimicrobial agent for plant disease management without altering the native soil microflora.