Nanoparticles have emerged as promising materials for a wide range of applications, including biomedicine, energy, and electronics. However, controlling their surface chemistry is essential to fully harnessing their potential, as it affects their physicochemical properties, stability, and interactions with biological systems. Surface functionalization is a key process enabling the adaptation of nanoparticle properties to specific applications. While introducing ligands during nanoparticle synthesis may not always be feasible, ligand exchange offers versatility in controlling surface chemistry. However, the direct replacement of negatively charged citrate on gold and silver nanoparticles with its positive counterparts often leads to particle aggregation. Here, we present a straightforward one-step ligand exchange method to functionalize citrate-coated gold and silver nanoparticles with cationic ligands. By controlling citrate molecule protonation, we prevent nanoparticle aggregation, enabling successful displacement with positively charged alkanethiol ligands. Dynamic light scattering, ζ-potential measurement, and transmission electron microscopy alongside theoretical models provide comprehensive insights into the mechanism and dynamics of ligand exchange. Furthermore, we demonstrate the impact of surface functionalization of nanoparticles on the cytotoxic activity of nanoparticles in model cell lines, underscoring the significance of the surface chemistry of nanoparticles for their biomedical applications.