Inspired by nature, green chemistry uses various biomolecules, such as proteins, as reducing agents to synthesize metallic nanostructures. This methodology provides an alternative route to conventional harsh synthetic processes, which include polluting chemicals. Tuning the resulting nanostructure properties, such as their size and shape, is challenging as the exact mechanism involved in their formation is still not well understood. This work reports a well-controlled method to program gold nanostructures' shape, size, and aggregation state using only one protein type, mucin, as a reduction and capping material in a one-pot bio-assisted reaction. Using mucin as a gold reduction template while varying its tertiary structure via the pH of the synthesis, we demonstrate that spherical, coral-shaped, and hexagonal gold crystals can be obtained and that the size can be tuned over three orders of magnitude. This is achieved by leveraging the protein's intrinsic reducing properties and pH-induced conformational changes. The systematic study of the reaction kinetics and growth steps developed here provides an understanding of the mechanism behind this phenomenon. We further show that the prepared gold nanostructures exhibit tunable photothermal properties that can be optimized for various hyperthermia-induced antibacterial applications.