The bell pepper is a vegetable with high antioxidant content, and its consumption is important because it can reduce the risk of certain diseases in humans. Plants can be affected by different types of stress, whether biotic or abiotic. Among the abiotic factors, there is saline stress that affects the metabolism and physiology of plants, which causes damage, decreasing productivity and quality of fruits. The objective of this work was to evaluate the application of selenium, silicon and copper nanoparticles and saline stress on the bioactive compounds of bell pepper fruits. The bell pepper plants were exposed to saline stress (25 mM NaCl and 50 mM) in the nutrient solution throughout the crop cycle. The nanoparticles were applied drenching solution of these to substrate (Se NPs 10 and 50 mg L−1, Si NPs 200 and 1000 mg L−1, Cu NPs 100 and 500 mg L−1). The results show that saline stress reduces chlorophylls, lycopene, and β-carotene in leaves; but increased the activity of some enzymes (e.g., glutathione peroxidase and phenylalanine ammonia lyase, and glutathione). In fruits, saline stress decreased flavonoids and glutathione. The nanoparticles increased chlorophylls, lycopene and glutathione peroxidase activity in the leaves; and ascorbate peroxidase, glutathione peroxidase, catalase and phenylalanine ammonia lyase activity, and also phenols, flavonoids, glutathione, β-carotene, yellow carotenoids in fruits. The application of nanoparticles to bell pepper plants under saline stress is efficient to increase the content of bioactive compounds in fruits.