Tomato (Solanum lycopersicum L.), a globally significant vegetable crop, faces a substantial threat from viral diseases, specifically Groundnut bud necrosis orthotospovirus (GBNV). Traditional approaches such as removal of infected plants, use of barrier crops, and insecticides have been employed but they have not proven to be consistently effective. Consequently, an alternative approach involving the stimulation of host resistance through the Plant Growth Promoting Rhizobacteria (PGPR) was adopted. From the previous study, B. subtilis (BST8), B. subtilis (Bbv57), and B. amyloliquefaciens (Ka1) were found to be effective against GBNV in cowpea. To enhance the shelf life of Bacillus spp. and improve the water retention capacity of tomato leaf surfaces, these bacteria were encapsulated within nanosilica, an identified host defense inducer. An effective inverse Pickering emulsion with a 2.5% (w/v) silica concentration was developed and characterized using diverse techniques, viz., phase contrast, scanning electron microscopy, confocal microscopy, contact angle goniometry, and variable angle ellipsometry. The prepared emulsion was then tested for its antiviral efficacy against GBNV in cowpea and tomatoes. Nanoencapsulated Bacillus consortia significantly reduced GBNV lesions in cowpea to 0.63 per leaf compared to the control (6.63). DAC-ELISA revealed a virus titer of 0.75 (3.33 times lower than the control), indicating antiviral efficacy. In tomato (var. PKM1), the consortia achieved an impressive 77.91% disease reduction (19% DSI) at 14 days post-inoculation (DPI), surpassing both nanoemulsion and consortia alone (DSIs: 67 and 30%, respectively). Nanoencapsulated Bacillus consortia demonstrated the lowest GBNV titer in tomatoes (0.86 vs control-3.32) through DAC-ELISA. This study introduces a promising strategy for the effective management of GBNV in cowpea and tomatoes using nanoencapsulated Bacillus consortia, underscoring its potential as an effective solution in crop protection.