Microchannel emulsification can produce droplets of uniform size at high throughput for wide-ranging applications in the food and drug industry. Mammalian cell encapsulation using emulsion-based systems is of significant interest for immobilized culture or transplantation applications. Microchannel emulsification has recently been applied to mammalian cell encapsulation using alginate. Here, we extend this approach to thermoresponsive hydrogels using chitosan as a model. The performance of the microchannel emulsification process was compared to a previously established stirred emulsification method for mesenchymal stromal cell encapsulation. Chitosan microbeads with controlled sizes ranging from 600 µm to 1500 µm in diameter at a coefficient of variation less than 10 % were obtained after adapting the microchannel system design, channel geometries and operating parameters that affect the capillary number. In a single pass through a 21 G syringe needle, the fraction of ruptured beads was significantly reduced for monodisperse microchannel-generated vs polydisperse stirred emulsion-generated beads of matching De Brouckere mean diameter. The viability of the immobilized cells immediately after the process was 95 % ± 2 % and no significant difference in cell survival and growth factor secretion was observed between microchannel and stirred emulsion-generated beads over 3 days of culture. Microchannel emulsification is a promising and scalable approach to microencapsulate mammalian cells in hydrogels that undergo temperature-dependent gelation.