There is growing interest in analyzing the effect of microenvironments, which may be mimicked through liquid-liquid phase separation (LLPS), on the reactivity of biological macromolecules. We report the encapsulation by microfluidics of the division protein FtsZ and a LLPS system inside microdroplets and their conversion into permeable vesicles (allowing ligand uptake), with higher yield, homogeneity and biomolecular compatibility than those previously described.