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Silver nanoparticles have gained considerable interest in recent decades due to their antimicrobial activity and are used in water disinfection, wound healing, food packaging, and plant protection. This study tested the potential of silver nanoparticles synthesized using the neem (Azadirachta indica) leaf extract against Alternaria solani causes early blight disease in tomato plants. The pathogen was isolated from infected tomato plants and identified using morphological and molecular features. The results showed significant variation among isolates. Isolates, Shk-1 and Ksr-1 were highly pathogenic, causing up to 80% disease incidence. The potential of silver nanoparticles against each isolate was determined using different concentrations of silver nanoparticles. During in vitro and in vivo experiments, the growth inhibition rate of the pathogen was 70–100% at 50 ppm. Lower concentrations of silver nanoparticles (5 and 10 ppm) increased phenolics, PO, PPO, and PAL production by more than 50% as compared to the untreated control. These defensive mechanisms clearly demonstrate the fungicidal potential of AgNPs and recommend their utilization in different crop protection programs.