We prepared Janus microspheres based on sodium alginate for the encapsulation of mesenchymal stem cells (MSC) in one compartment and iron oxide nanoparticles (IONP) or a drug in the second compartment. 4% percent sodium alginate solution was allowed to pass through a septum-theta capillary device and react with 2.5% calcium chloride to allow crosslinking to occur in the solution, forming calcium alginate Janus microspheres. Physico-chemical characterization of microspheres was done by FTIR, TGA, and XRD after loading of stem cells and IONP/drug. The mechanical integrity of microspheres was tested at different time points, which showed that 4% alginate microspheres were mechanically stable for a long period of time. Live/dead staining of MSCs alone and the MTS assay of MSCs and DMSO co-loaded were performed, which showed less toxicity to MSC in the Janus configuration. IONP/MSC-loaded Janus microspheres were tested by magnetic manipulation for targeted MSC delivery for cartilage repair using an electromagnetic manipulation (EMM) device. Janus microspheres can be used for targeted stem cell/drug delivery using EMM for cartilage repair in the near future.