Liquid–liquid phase separation underlies the formation of biomolecular condensates and membraneless compartments in living cells. Physically, condensed liquid biomolecular systems represent water-in-water emulsions with a very low surface tension. Such emulsions are commonly unstable towards coalescence, yet in order to be functional, they must persist inside the cell. This observation thus raises the fundamental question of the origin of the stability of such emulsions, and whether passive physical mechanisms exist that stabilize droplets against fusion or coalescence. Here, through measurement of condensate zeta potentials on a single droplet level, we show that surface electrostatic properties of condensates can be used to describe and assess the emulsion stability of condensed liquid biomolecular systems. We find that condensates formed from a representative set of peptide/nucleic acid and protein systems have zeta potentials in the stability range predicted by classical colloid theory. Specifically, we describe the electrostatic nature of PR25:PolyU and FUS condensates and show that their zeta potentials correlate well with their propensity to fuse, coalesce, and cluster. Further, we bring together experiments with multiscale molecular simulations and demonstrate that the differences in zeta potential and subsequent stability of biomolecular condensates are modulated by their internal molecular organization. Taken together, these findings shed light on the origin of the stability of biomolecular condensate systems, and connect the organization of molecular-level building blocks to the overall stability of phase-separated biomolecular systems.