Droplet microfluidics is combined with bio-orthogonal thiol-ene click chemistry to fabricate micrometer-sized, monodisperse fibrinogen-containing hyaluronic acid hydrogel microbeads in a mild, radical-free procedure in the presence of human mesenchymal stem cells (hMSCs). The gel beads serve as microniches for the 3D culture of single hMSCs, containing hyaluronic acid and additional fibrinogen for cell surface binding, and they are porous and stable in tissue culture medium for up to 4 weeks with mechanical properties right in the range of soft solid tissues (0.9-9.2 kPa). The encapsulation procedure results in 70% viable hMSCs in the microbeads after 24 hours of culture and a very high degree of viability of the cells after long term culture of 2 weeks. hMSCs embedded in the microniches display an overall rounded morphology, consistent with those previously observed in 3D culture. Upon induction, the multipotency and differentiation potential of the hMSCs are characterized by staining of corresponding biomarkers, demonstrating a clear heterogeneity in the cell population. These hydrogel microbeads represent a versatile microstructured material platform with great potential for studying the differences of material cues and soluble factors in stem cell differentiation in a 3D tissue-like environment at the single cell level.