Quantum dots (QDs) are presently studied intensively as fluorescent probes for biomedical applications due to their high emission quantum yield, excellent resistance to photobleaching, photostability, and large Stokes shift, when contrasted with commonly utilized organic fluorescent dyes. This study introduces a protein engineering approach to incorporate metal coordination sites for the sustainable synthesis and stabilization of biocompatible CdS QDs in proteins. The resulting protein-stabilized CdS QDs (Prot-QDs), generated by a green aqueous route at 37 °C, are highly photoluminescent and photostable, have a long shelf life, and present high stability under physiological conditions. The Prot-QDs showed effective internalization and high fluorescence in cells, even at low doses and biocompatibility. This work focuses on CdS QDs, since this composition has been extensively studied, however this approach could be easily translated to QDs with other metal composition. Here, protein design emerges as a promising approach to generate protein–hybrid nanomaterials as broadly applicable tools in different applications such as light-emitting devices, metal ion detection, and biomedical applications.