The unique advantages of quantum dot (QD) bioconjugates have motivated their application in biological assays. However, physical characterization of bioconjugated QDs after surface modification has often been overlooked. Here, biotinylated antibodies (biotin-IgG) were attached to commercial streptavidin-conjugated quantum dots (strep-QDs) at different stoichiometric ratios, and these QD bioconjugates were characterized with atomic force microscopy and discontinuous sodium dodecyl sulfate agarose gel electrophoresis (SDS-AGE). The results from these complementary analytical techniques showed that the molar ratio determined the relative sizes, molecular weights and morphologies of the QD bioconjugates. Additionally, the novel discontinuous SDS-AGE analysis confirmed specific binding between biotin-IgG and strep-QDs. Researchers who design QD bioconjugates for cell-based assays should consider stoichiometry-dependent differences in the physical properties of their QD bioconjugates.