Here we report on the design and characterization of calcium-alginate microgels (MGs) containing positively charged iron oxide nanoparticles (IONPs) and negatively charged oil-in-water (O/W) nanocarriers (NCs). To provide ionic compatibility of IONPs with the negatively charged NCs and alginate in MGs, they were coated with the anionic polysaccharides alginate, carrageenan or sulfobutyl-β-cyclodextrin. The mixing of both nanostructures (coated-IONPs and O/W NCs) with alginate solutions provide homogeneous dispersions able to form spherical hydrogels with different sizes (250-1400 micrometers) and encapsulating the nanostructures with high efficiency. MGs loaded with both nanostructures were reactive to continuous (attractive interaction) and alternating magnetic field (heat release similar to non-encapsulated IONPs). The encapsulation of both nanostructures in MGs was maintained even after 7 days of storage at 40 °C. We postulate that the above results will be of interest for the design of hydrogel formulations with therapeutic applications.