This study employs nanoengineering techniques to enhance the aqueous compatibility of andiroba oil and ginger extract, both renowned for their phytotherapeutic properties, aiming at biomedical applications. The natural products were characterized using HPLC-MS, CG-MS, UV-Vis, and FTIR. Optimal surfactant concentrations (lecithin and Tween® 20) were established to produce more biocompatible and stable oil-in-water nanoemulsions. The nanodroplets were characterized at multiple hierarchical levels, including their shape (spherical), size (∼130 nm), polydispersity (PDI = 0.20), and surfactant interfacial film architecture through a cross-analysis of DLS, ELS, SAXS, TGA, UV-Vis, and FTIR. Zetametry and DLS were used to investigate the mechanism of colloidal stabilization of the nanodrops and evaluate the stability of the nanoemulsion under varying pH and ionic strength conditions during storage at different temperatures. The quantification of phenol and flavonoids, coupled with assessments of antioxidant activity, demonstrated an additive effect, indicating that both andiroba oil and ginger extract retain their significant antioxidant efficacy within the nanoemulsion formulation. The effect of the nanoformulation on the viability and morphology of mouse fibroblast NIH-3T3 was also examined. The IC50 of the nanoemulsion at 48 h (765 μg/ml) is higher than the values reported for other nanoemulsions of andiroba oil or ginger extract. This innovative nanoemulsion system combining andiroba oil and ginger extract offers the potential for additive or synergistic effects while exerting minimal impact on healthy cell viability.