The emerging applications for hydrogel materials at different length scales, in areas ranging from sustainability to health, has driven the progress in the design and manufacturing of microgels. Microgels can provide miniaturized, monodisperse, and regulatable compartments, which can be spatially separated or interconnected. These microscopic materials provide novel opportunities for providing biomimetic cell culture environments and are thus key to the advances of modern biomedical research. The evolution of our understanding of the physical and chemical properties has, furthermore, highlighted the potentials of microgels in the context of materials science and bioengineering. This review describes the recent research progress in the fabrication, characterization, and applications of microgels generated from biomolecular building blocks. A key enabling technology allowing the tailoring of the properties of microgels is their synthesis through microfluidic technologies and we highlight recent advances in this areas and their impact on expanding the physicochemical parameter space accessible using microgels. We finally discussed the emerging roles that microgels play in liquid–liquid phase separation, micromechanics, biosensors, and regenerative medicine.