Plant-derived natural bioactive molecules are of great therapeutic potential but, so far, their application in nanomedicine has scarcely been studied. This work aimed at comparing two methodologies, i.e., adsorption and in situ incorporation, to prepare hybrid polyphenol/hydroxyapatite nanoparticles. Two flavonoids, baicalin and its aglycone derivative baicalein, and two phenolic acids derived from caffeic acid, rosmarinic and chlorogenic acids, were studied. Adsorption of these polyphenols on pre-formed hydroxyapatite nanoparticles did not modify particle size or shape and loading was less than 10% (w/w). In contrast, presence of polyphenols during the synthesis of nanoparticles significantly impacted and sometimes fully inhibited hydroxyapatite formation but recovered particles could exhibit higher loadings. For most hybrid particles, release profiles consisted of a 24 h burst effect followed by a slow release over 2 weeks. Antioxidant properties of the polyphenols were preserved after adsorption but not when incorporated in situ. These results provide fruitful clues for the valorization of natural bioactive molecules in nanomedicine.