Aquasomes (AQ) are self-assembled nanostructures, made up of a spherical hydroxyapatite core and a carbohydrate layer on top, for delivering bioactive molecules like proteins, peptides, etc., which are adsorbed on the carbohydrate layer. This is the first report of its kind demonstrating AQ as an efficient dual drug delivery system, capable of releasing bioactive molecule and a hydrophobic drug together. The synthesized AQ before and after adsorption of the bioactive molecule are characterized using dynamic light scattering, scanning electron microscopy, X-ray diffraction, small-angle X-ray scattering, Fourier transform infrared spectroscopy, thermogravimetric analysis, differential scanning calorimetry, and Raman spectroscopy. BSA (bovine serum albumin) protein is used as the model bioactive molecule for the in vitro dual release studies along with representative hydrophobic drugs Coumarin 153 (C153), Warfarin (WAR), and Ibuprofen (IBU). The release behaviors of the hydrophobic drugs are explained by studying their binding interactions with BSA. The binding interactions of the drugs with BSA are analyzed by carrying out fluorescence quenching experiment of BSA, site marking competition experiment, anisotropy, and E T (30) studies. Further, in vitro biocompatibility studies are performed for dually loaded AQ by using hemolysis assay. The hemolysis assay do not show any lysing of the red blood cells, suggesting the formulations to be clinically capable for administration.