Nanoparticles (NPs) have the potential to improve plant health and secondary metabolite production. In the present study, three different NPs, i.e., Ag, Cu, and Cu-Ag NPs were produced in the range from 25 to 86 nm, with zeta potentials ranging from -28.8 to -38.5 mV. The synthesized NPs were used for seed priming and foliar spray on three varieties of Capsicum annuum. L, i.e., Arka Sweta (AS), Arka Meghana (AM), and Arka Harita (AH) plants grown under greenhouse conditions. Seed priming at various concentrations of NPs (1, 10, 20 ppm) enhanced the seed germination (96%), seedling vigor index (2494-3112.66), seedling length (6-49%), and biomass (46%) of 45 days old Arka Meghana seedlings. Additionally, all plant tissues accumulated significantly higher amounts of chlorophyll (51-142%), carotenoids (23-94.2%), total phenolic content (73%), and total flavonoid content (57%), compared with the control (p ≤ 0.05). The foliar spray of NPs (20-100 ppm) has a protective effect on the chili plants against thrips infestation (30-76%). The foliar spray enhanced chlorophyll (15-62%), carotenoids (15-50%), total phenolic content (20-62%), total flavonoid content (64-99%), reducing sugars (15-97%), total antioxidant activity (15-142%), ferric reducing antioxidant power assay (15-109%), DPPH (129-54 mg mL-1), and capsaicinoids (capsaicin and dihydrocapsaicin) (82-128%). This study illustrates that Ag, Cu, and Cu-Ag NPs suppress thrips infestation and proliferation with enhanced plant growth and biochemical activity, which is inversely proportional to the NP size. Chemical NPs play a crucial role in the economic significance of chili plants, offering a promising avenue for developing pesticides to effectively combat thrips infestation. This advancement holds great potential in enhancing the overall agronomic productivity of the chili crops.