We report the development and application of an analytical system consisting of capillary electrophoresis (CE) interfaced with inductively coupled plasma mass spectrometry (ICP-MS) for sensitive and high-resolution characterization of quantum dots (QDs) interacting with serum proteins. Separation resolution between the intact CdSeS/ZnS QDs and their protein conjugates was optimized by varying the type and concentration of background electrolyte, applied voltage, and sample loading. Special attention was paid to the CE system compatibility with physiological conditions, avoiding aggregation effects, and analyte recovery. Optimization trials allowed for acquiring satisfactory stability of migration times (within 6.0% between different days), peak area precision of 5.2–8.0%, capillary recoveries in the range of 90–96%, and a lower limit of detection of 7.5 × 10⁻⁹ mol L⁻¹ Cd. With the developed method distinct metal-specific profiles were obtained for the QDs in combination with individual serum proteins, their mixtures, and in human serum. Particularly, it was found that albumin binding to the particle surface is completed after 1 h, without noticeable disruption of the core–shell integrity. The transferrin adsorption is accompanied by the removal of the ZnS shell, resulting in evolving two different metal–protein conjugated forms. On the other hand, proteinization in real-serum environment occurs without binding to major transport proteins, the QDs also lose their the shell (the higher the dose the longer is the time they stay unbroken). The concomitant changes in migration behavior can be attributed to interactions with serum proteins other than albumin and transferrin. Speciation information provided by CE-ICP-MS may shed light on the mechanism of QD delivery to the target regions of the body.