To understand how membrane-free subcompartmentalization can modulate biochemical reactions by coupled spatial enzyme localization with substrate and product partitioning, we use microfluidic strategies to synthesize, stabilize and characterize micron-sized functional coacervates in water−oil emulsions. Our methodologies have allowed for the first time to quantitatively characterize partition coefficients of a broad range of different molecules with different coacervate chemistries and to measure reaction rates of individual subcompartments and their surrounding aqueous environment at the single coacervate level. Our results show that sub-compartmentalisation increases the overall rates of reactions. This bottom-up synthetic strategy for the production of synthetic organelles offers a physical model for membrane-free compartmentalization in biology and provides insights into the role of sub-compartmentalisation in regulating out-of-equilibrium behaviours in biological systems.