This study fabricated a novel biohybrid microgel containing polysaccharide-based polyelectrolyte complexes (PECs) for anthocyanins. Herein, anthocyanins were encapsulated into PECs composed of chondroitin sulfate and chitosan, followed by incorporation into alginate microgels using emulsification/internal gelation method. We demonstrated that PECs incorporation strongly affected the properties of microgels, dependent on the polysaccharide concentration and pH in which they were fabricated. The dense internal network surrounded by an alginate shell was clearly visualized in cross-sectioned PECs-microgels. Stability studies carried out under varying ionic strength and pH conditions demonstrated the stimuli-responsiveness of the PECs-microgels. Additionally, the presence of PECs conferred microgels with high rigidity during freeze-drying and excellent reconstitution capacity upon rehydration. These observations were attributed to the modulation of electrostatic and hydrogen-bonding cross-linking between PECs and the alginate gel matrix and suggest the PECs inclusive microgels hold promise as delivery vehicles for the controlled release of hydrophilic bioactive compounds.