Creating new environmentally friendly and non-toxic biomaterials with novel properties is required for numerous applications in healthcare and sensing. Protein bound gold nanoclusters constitute one such class of materials that offer promise in fluorescence imaging and sensing applications. However, unlike alkane thiol-protected gold nanoclusters, the number of protein-templated gold nanoclusters with such properties is limited and there is a need to expand the repertoire of such attractive hybrid quantum clusters. Herein, we report the synthesis, characterization, and applications of new fluorescent gold nanoclusters with tunable emission properties including blue, orange, and red, within a four-helix bundle copper storage protein (Csp1). The template protein consists of 13 cysteines along the length of the helix, which are suitable ligands to template Au and stabilize the resulting 14–19 atom clusters within the protein. The resulting clusters were extensively characterized by employing spectroscopic, microscopic and other analytical methods. The optical emission, relative quantum yields, and the excited state lifetime of the clusters are shown to depend on synthetic conditions. The clusters were found to be sensitive to the ppm level of transition metal ions with the quenching capabilities following the Irving–Williams series of metals (Co²⁺ < Ni²⁺ < Cu²⁺), which is rationalized based on the relative affinities of transition metals for a given set of ligands. The clusters were also found to be stable across the pH range 4–8.5 which, along with tunable emission properties paves the path for live bio-imaging and bio-sensing applications under physiological conditions.