Microfluidic flow cells provide excellent control over the formation of microemulsions, which are widely applied as templates for the fabrication of hydrogel microparticles and vesicles with defined physicochemical properties. In recent years, bio-orthogonal synthesis schemes of macromolecular building blocks as well as their microfluidic processing under mild reaction conditions have greatly extended microfluidics-based vesicle and hydrogel design beyond material sciences. In particular, in synthetic and cell biology, tissue engineering as well as cell-free biotechnology, microgels and vesicles as experimental platforms with known parameter space allow for mimicking, studying and manipulating key aspects of cellular life in vitro in a tailored fashion. This article provides insights in recent advances to fabricate vesicles and microgels by microfluidic jets and droplets with tailored volume, shape and internal structure, and presents developments in applying these materials as artificial extracellular matrices as well as simple cell mimics designed by microfluidics.