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Proteins can template the heterogeneous nucleation and growth of size-confined nanocrystals. However, protein-templated mineralization often leads to particles that exhibit low colloidal stability, poor crystal quality, and/or diminished photoluminescence. Here, we report protein cage–spherical nucleic acids (SNAs) that can be used as nanoreactors for quantum dot (QD) synthesis and subsequent intracellular delivery. The resulting QD-SNA structures are monodisperse, colloidally stable, and photoluminescent in aqueous solution. The nanoreactors were prepared using two different proteins (~10 and 12 nanometers in diameter), and CdS, CdSe, and PbSe nanocrystals were synthesized. Moreover, the extent of surface defects and crystallinity depends on the relative concentrations of ionic precursors, which control the growth rate and the number of ionic vacancies. By optimizing conditions, CdS-SNAs that exhibit near-zero reabsorption loss were synthesized. Last, QD-SNAs exhibit enhanced cellular uptake and minimal cytotoxicity when compared to commercial QD-protein conjugates, making them potentially useful in bioimaging and diagnostic applications.