We demonstrate the in-droplet separation and enrichment of molecules from small organic molecules to long nucleic acids (lambda DNA). Electric potentials are applied via two parallel three-dimensional electrodes, which interface the nanodroplets through polydimethylsiloxane (PDMS)-carbon composite membranes. These membranes enable the generation of uniform electric fields inside the droplets, while simultaneously preventing the formation of electrolytic byproducts. Biomolecules of different sizes migrate toward one side of the droplets, according to their net charge, when exposed to the electric field. Directly afterward, a Y-junction promotes droplet splitting, resulting in the generation of biomolecule-enriched daughter droplets. Biomolecules were fluorescently labeled, and fluorescence microscopy was employed to assess their electrophoretic separation and enrichment. Experimental results demonstrate how the enrichment of biomolecules is influenced by their size, charge, and concentration, by the ionic strength, viscosity, and pH of the suspending medium, and by the in-droplet flow profile. Enrichments above 95% were observed for small molecules and highly charged species at velocities over 10 mm/s (13 droplets per second). Moreover, the enrichment performance asymptotically approached a value of 38% for velocities as high as 50 mm/s, demonstrating the potential of this technique for the high-throughput separation of charged species. The applicability of the system was demonstrated by cleaving a peptide and selectively separating the cleaved fragments in different daughter droplets on the basis of their net charge.