In the present study, magnetically Fe3O4/SiO2/hydroxyapatite (Fe3O4/SiO2/HAp) nanocomposites were synthesized and modified with 3-aminopropyl triethoxysilane (APTES) using fructose as a green capping agent. The effect of different capping agent (such as fructose and glucose) and calcination temperature were investigated to reach optimum condition. The as-prepared nanocomposites were characterized by XRD, FT-IR, SEM, EDS, TEM, DLS, VSM and N2 adsorption-desorption isotherm technique. The as-prepared nanocomposites have been used as atenolol controlled carrier due to their advantage such as high pore size (13.37 nm) and large surface area (55.88 m2 g-1). The drug release was studied in the gastrointestinal tract (intestine and stomach) pH-similar milieu. The results show that 100% and 15.6% of impregnated atenolol could be released from Fe3O4/SiO2/HAp functionalized with APTES after 30 h at pH = 6.8 and pH 1.2, respectively. Also, the histopathological experiment shows that abnormality of the liver, spleen and kidney was observed after 48 h study.