Propolis has health beneficial properties attributed to its phenol composition. Although, it has low water solubility, strong taste, and aroma, limiting its application in the food industry. This study explores the stabilization of phenolic compounds from propolis extract (PE) during the production of potato and cassava starch nanoparticles (NPs) by antisolvent precipitation. Phenolic content and antioxidant capacity (ABTS and DPPH) of acidified PE obtained with different ethanol concentrations are determined. Starch NPs based on cassava and potato starch are characterized in terms of physicochemical properties, including loading efficiency, particle size distribution and surface charge, moisture content, water activity, chemical bonds, crystalline structure, thermal stability, color, and solubility in water. Fourier‐transform infrared spectra and X‐ray diffractograms reveal that the phenolic compounds of PE are stabilized with the starch NPs, in this way, at least 54.91% of phenolic compounds from PE are stabilized by the starch NPs. Starch NPs stabilizing the phenolic compounds display brown color and high solubility in hot water (90 °C). This research reports for the first‐time information regarding the stabilization of phenolic compounds from PE using starch NPs. These starch NPs have a great potential to be used in food formulations or to manufacture active food packaging.