Thiol-ene polymerization has been pointed out as a promising technique to produce biobased polymers for biomedical applications due to its advantages, including mild conditions and rapid reaction rates without the formation of byproducts. Therefore, in this study different concentrations of magnetic nanoparticles (MNPs) were incorporated in poly(thioether-ester) (PTEE) nanoparticles by thiol-ene miniemulsion polymerization of biobased monomers to form both linear and branched cross-linked polymers. Loading efficiencies up to approximately 95% (thermogravimetric analysis) of the MNPs within the polymer matrix were obtained. In addition, the substitution of the dithiol 1,4-butanedithiol (64.2%) for the tetrathiol PTEMP (95.8%), increased the encapsulation efficiency by about 30%. Hybrid nanoparticles presented average mean diameters between 95 and260 nm with polydispersity index between 0.13 and 0.42 by DLS, negative zeta potentials around −45 mV and superparamagnetic behavior. The hyperthermia assays performed on breast cells (MDA-MB 231) have shown that the cell death was dependent on the exposure time to the AC magnetic field and the reduction in cell viability was approximately 35%. These results demonstrated the production of superparamagnetic PTEE nanoparticles via thiol-ene polymerization and highlight the promising application of these biobased materials for cancer treatment by hyperthermia.