The wilt complex is one of the most important pomegranate diseases after bacterial blight, affecting pomegranate cultivation in all major growing regions of India. Given its significance, the study was designed to synthesis green nanoparticles, i.e., Pseudomonas fluorescens-based zinc nanoparticles (Pf-ZnNPs), Chitosan-based zinc nanoparticles (Ch-ZnNPs), pomegranate aril-based sulphur nanoparticles (PA-SNPs), and pomegranate peel-based silver nanoparticles (PP-AgNPs) for the management of pomegranate wilt complex. The synthesised nanoparticles were characterised using a particle size analyzer (PSA), a scanning electron microscope (SEM), and energy dispersive X-ray spectroscopy (EDS). Among the four nanoparticles, Pf-ZnNPs recorded the lowest mean diameter of 9.9 ± 5.4 nm with a spherical shape. In the in vitro evaluation of the different nanoparticles (100 ppm to 1500 ppm concentrations), P. fluorescens based ZnNPs (Pf-ZnNPs) showed equally effective antifungal activity on Ceratocystis fimbriata and Fusarium oxysporum with maximum mycelial inhibition of 84.74 and 86.04%, respectively, at 1500 ppm concentration. Further Pf-ZnNPs were tested in the pot experiment as well as in the field.