In this work, biocompatible and degradable biohybrid microgels based on chitosan and dextran were synthesized for drug delivery applications. Two kinds of bio-based building blocks, alkyne-modified chitosan and azide-modified dextran, were used to fabricate microgels via single-step cross-linking in water-in-oil emulsions. The cross-linking was initiated in the presence of copper(II) without the use of any extra cross-linkers. A series of pH-responsive and degradable microgels were successfully synthesized by varying the degree of cross-links. The microgels were characterized using H-1 NMR and FTIR spectroscopy which proved the successful cross-linking of alkyne-modified chitosan and azide-modified dextran by copper(II)-mediated click reaction. The obtained microgels exhibit polyampholyte character and can carry positive or negative charges in aqueous solutions at different pH values. Biodegradability of microgels was shown at pH 9 or in the presence of Dextranase due to the hydrolysis of carbonate esters in the microgels or 1,6-alpha-glucosidic linkages in dextran structure, respectively. Furthermore, the microgels could encapsulate vancomycin hydrochloride (VM), an antibiotic, with a high loading of approximately 93.67% via electrostatic interactions. The payload could be released in the presence of Dextranase or under an alkaline environment, making the microgels potential candidates for drug delivery, such as colon-specific drug release.