Propolis natural extracts have been used since ancient times due to their antioxidant, anti-inflammatory, antiviral, and antimicrobial activities. In this study, we produced scaffolds of type I collagen, extracted from Wistar Hanover rat tail tendons, and impregnated them with propolis nanoparticles (NPs) for applications in regenerative medicine. Our results show that the impregnation of propolis NPs to collagen scaffolds affected the collagen denaturation temperature and tensile strength. The changes in structural collagen self-assembly due to contact with organic nanoparticles were shown for the first time. The fibril collagen secondary structure was preserved, and the D-pattern gap increased to 135 ± 28 nm, without losing the microfiber structure. We also show that the properties of the collagen scaffolds depended on the concentration of propolis NPs. A concentration of 100 μg/mL of propolis NPs with 1 mg of collagen, with a hydrodynamic diameter of 173 nm, was found to be an optimal concentration to enhance 3T3 fibroblast cell metabolic activity and cell proliferation. The expected outcome from this research is both scientifically and socially relevant since the home scaffold using natural nanoparticles can be produced using a simple method and could be widely used for local medical care in developing communities.