Cell microencapsulation holds great promise as a therapeutic strategy for the controlled and sustained delivery of biologically relevant agents. The authors developed cell-laden microgel scaffolds with excellent long-term viabilities by combining bioorthogonal strain promoted azide-alkyne cycloaddition (SPAAC) and droplet-based microfluidic templating. Star-shaped polyglycerol hexaazide, alpha,omega-bis azido-linear polyglycerol or polyethylene glycol as well as dendritic polyglycerol-(polycyclooctyne) served as bioinert hydrogel precursors. The authors demonstrate for the first time the generation of entirely polyglycerol-based microcapsules with excellent stability and full retention of viability of the packed cells for longer than 3 weeks. As a result, our microgel particles could be used for long-term immunoisolation of cells enabling their study during encapsulation.