Surface modification of superparamagnetic iron oxide nanoparticles (SPIONs) has been introduced with lauric acid and oleic acid via co-precipitation and thermal decomposition methods, respectively. This modification is required to increase the stability of SPIONs when incorporated in hydrophobic, biodegradable and biocompatible polymers such as poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). In this work, the solid-in-oil-in-water (S/O/W) emulsion-solvent extraction/evaporation method was utilized to fabricate magnetic polymer microspheres incorporating SPIONs in PHBV. The prepared magnetic PHBV microspheres exhibited particle sizes <1 µm. The presence of functional groups of lauric acid, oleic acid and iron oxide in the PHBV microspheres was confirmed by Fourier Transform Infrared spectroscopy (FTIR). X-ray diffraction (XRD) analysis was performed to further confirm the success of the combination of modified SPIONs and PHBV. Thermogravimetric analysis (TGA) indicated that PHBV microspheres were incorporated with SPIONsLauric as compared with SPIONsOleic. This was also proven via magnetic susceptibility measurement as a higher value of this magnetic property was detected for PHBV/SPIONsLauric microspheres. It was revealed that the magnetic PHBV microspheres were non-toxic when assessed with mouse embryotic fibroblast cells (MEF) at different concentrations of microspheres. These results confirmed that the fabricated magnetic PHBV microspheres are potential candidates for use in biomedical applications.