Proteins are widely utilized as templates in biomimetic synthesis of gold nanocrystals. However, the role of proteins in mediating the pathways for gold nucleation and growth is not well understood, in part because of the lack of spatial resolution in probing the complicated biomimetic mineralization process. Self-assembled protein cages, with larger size and symmetry, can facilitate in the visualization of both biological and inorganic components. We have utilized bacteriophage P22 protein cages of ∼60 nm diameter for investigating the nucleation and growth of gold nanocrystals. By adding a gold precursor into the solution with preexisting protein cages and a reducing agent, gold nuclei/prenucleation clusters form in solution, which then locate and attach to specific binding sites on protein cages and further grow to form gold nanocrystals. By contrast, addition of the reducing agent into the solution with incubated gold precursor and protein cages leads to the formation of gold nuclei/prenucleation clusters both in solution and on the surface of protein cages that then grow into gold nanocrystals. Because of the presence of cysteine (Cys) with strong gold-binding affinity, gold nanocrystals tend to bind at specific sites of Cys, irrespective of the binding sites of gold ions. Analyzing the results obtained using these alternate routes provide important insights into the pathways of protein-mediated biomimetic nucleation of gold that challenge the importance of incubation, which is widely utilized in the biotemplated synthesis of inorganic nanocrystals.