Most high-quality quantum dots (QDs) are synthesized in the organic phase, and are often coated with polymers for use in aqueous biological environments. QDs can exhibit fluorescence losses during phase transfer, but evaluating underlying mechanisms (e.g., oxidation, surface etching, loss of colloidal stability) can be challenging because of variation in synthesis methods. Here, fluorescence stability of QDs encapsulated in block co-polymer (BCP) micelles was investigated as a function of BCP terminal functionalization (i.e., -OH, -COOH, and -NH2 groups) and synthesis method (i.e., electrohydrodynamic emulsification-mediated selfassembly (EE-SA), sonication, and manual shaking). Fluorescence losses, fluorescence intensity, energy spectra, and surface composition were assessed using spectrofluorometry and cathodoluminescence spectroscopy (CL) with integrated X-ray photoemission spectroscopy (XPS). QDs passivated using charged BCPs exhibited 50-80% lower fluorescence intensity than those displaying neutral groups (e.g., -OH), which CL/XPS revealed to result from oxidation of surface Cd to CdO. Fluorescence losses were higher for processes with slow formation speed, but minimized in the presence of poly(vinyl alcohol) (PVA) surfactant. These data suggest slower BCP aggregation kinetics rather than electrostatic chain repulsion facilitated QD oxidation. Thus, polymer coating method and BCP structure influence QD oxidation during phase transfer and should be selected to maximize fast aggregation kinetics.