A strategy to incorporate and release the amphiphilic drugs of doxorubicin (DOX) and ibuprofen (IBU) in the same microcapsules is introduced, A layer-by-layer (LbL) assembly of microcapsules with doxorubicin hydrochloride (DOX) or green fluorescent agent, hydrophilic fluorescein isothiocyanate (FITC), encapsulated in CaCO3 microparticle templates, was conducted via alternatively depositing sodium carboxymethyl cellulose (CMC) and chitosan (CHI) onto IBU or red fluorescent agent (hydrophobic Nile Red) preloaded poly-L-lactide (PLLA) coated magnetic Fe3O4-DOX-loaded CaCO3 (or RTCloaded) templates. The structure, morphology, composition, magnetic properties and drugs distribution of the obtained microcapsules were characterized by nuclear magnetic resonance (NMR), scanning electron microscopy (SEM), zeta potential analysis, thermogravimetric analysis (TGA), vibrating sample magnetometry (VSM) and confocal laser scanning microscopy. The fluorescent agents loading of RTC and Nile Red were confirmed by observations using confocal laser scanning microscopy. Fluorescence observations showed that the DOX was distributed both in the walls and in the cavities of the microcapsules, while IBU was present in the capsule wall. The in-vitro release of the dual drugs, DOX and IBU, from the microcapsules with different numbers of CHI and CMC layers was characterized. A tunable amount of drug release was achieved by changing the number of layers. The release study indicated that the LBL microcapsules exhibited better sustained release capacity compared to the uncoated microcapsules. The microcapsules inherited a strong magnetic property from the Fe3O4 nanoparticles, sufficient for targeting and magnetic hyperthermia drug delivery systems.