The intentional introduction of transition metal impurities in semiconductor nanocrystals is an attractive approach for tuning quantum dot emission over a wide range of wavelengths. However, the development of effective doping strategies can be challenging, especially if one simultaneously requires a low-toxicity crystalline core, a functional protein shell, and a "green", single-step synthesis process. Here, we describe a simple and environmentally friendly route for the biofabrication of Cu-doped (blue-green) or Mn-doped (yellow-orange) ZnS nanocrystals surrounded by an antibody-binding protein shell. The ZnS:Mn hybrid particles obtained with this method exhibit a 60% enhancement in maximum photoluminescence intensity relative to undoped nanocrystals and have a hydrodynamic diameter inferior to 10 nm. They can be stored for months at 4 °C, are stable over a physiological range of pH and salt concentrations, can be decorated with variable amounts of antibodies by direct mixing, and hold promise for biosensing and imaging applications.