The methodological developments and applications of CE related to studying biotransformations of metal-based nanoscale particles of impending medicinal use are overviewed. This is an update to a previous review article (Aleksenko, S. S., Shmykov, A. Y., Oszwaldowski, S., Timerbaev, A. R., Metallomics 2012, 4, 1141-1148) and it covers the research papers published within the last five years. As was anticipated in that review, CE can now be seen as a customary technique in the analysis of biomolecular interactions that exert an impact on the mechanism of action of nanoparticles, comprising metabolism, delivery, cell processing, and targeting. Different ways by which the CE method is applied for such monitoring, including conjugation mode, sample preparation, separation, and detection, are critically assessed. Special emphasis is put on examinations using inductively coupled plasmaMS detection recent advent of which to the area made CE a versatile speciation tool for biomedical studies of nanomaterials containing metals.