Peppers are consumed all over the world due to the flavor, aroma, and color that they add to food. Additionally, they play a role in human health, as they contain a high concentration of bioactive compounds and antioxidants. The treatments used were an absolute control, Cs-PVA, and four treatments with 0.02, 0.2, 2, and 10 mg (nCu) g−1 (Cs-PVA). The application of Cu nanoparticles in chitosan-PVA hydrogels increases the content of capsaicin by up to 51% compared to the control. This application also increases the content of antioxidants ABTS [2,2′-azino-bis (3-ethylbenzothiazolin-6-sulfonic acid)] and DPPH (2,2-diphenyl-1-picrylhydrazyl), total phenols and flavonoids (4%, 6.6%, 5.9%, and 12.7%, respectively) in jalapeño pepper fruits stored for 15 days at room temperature; under refrigeration, it increases DPPH antioxidants, total phenols, and flavonoids (23.9%, 1.54%, and 17.2%, respectively). The application of Cu nanoparticles in chitosan-PVA hydrogels, even when applied to the substrate, not only has an effect on the development of the jalapeño pepper crop, but also modifies the post-harvest characteristics of the jalapeño pepper fruits.