Combinatorial techniques have made possible the isolation of polypeptides that bind to materials of technological interest including metals, metal oxides, chalcogenides, and semiconductors. Such inorganic binding peptides (IBPs) not only adsorb to the surfaces against which they have been selected, but may also influence materials nucleation, growth, and morphology, and thus, functional properties. To better control IBP solubility, facilitate their production and purification, and specify how they are presented to the solution or surface, we engineer these small peptides within the framework of larger proteins. The resulting designer proteins combine biological function of the host scaffold with the adhesive or synthesizing properties of the guest peptide. However, while the arsenal of designer proteins is growing, our fundamental understanding of protein-aided synthesis remains in its infancy. First, we exploit the ability of electrodeposition to decouple materials nucleation and growth to study how designer proteins control inorganic morphogenesis. We specifically show that a silver-binding designer protein (MBP-Ag4) promotes the growth of rosette-like silver particles under conditions where our controls yield pentagonally twinned crystals. The difference in growth habit is correlated to specific interactions between the designer protein and the {111} faces of polycrystalline silver nuclei. Second, we focus on solution phase nucleation and growth and describe a micro-reactor allowing for parsimonious use of designer proteins in controlled nanoparticle manufacturing. We develop and validate a finite element simulation of how reactant concentrations vary with residence time and position, use this tool to model a reaction with fast kinetics, and compare results to the synthesis of borohydride reduced silver nanoparticles in the presence of citrate. Third, we use the same device and chemistry, but substitute designer proteins for citrate, to systematically investigate how IBP identity, designer protein concentration and residence time affect the size, concentration, and morphology of silver nanoparticles. We demonstrate that for this fast kinetic reaction with a large potential driving force, particle concentration correlates with residence time and that designer proteins are critical to exert size control. Finally, we suggest the next generation of experiments based on a details comparison of our microfluidic and electrodeposition experiments.