Control of ionomer thin film structures on metal surfaces is pivotal for efficient performance in electrochemical devices such as fuel cells and electrolyzers. Unfortunately, the assembly of these thin film structures is difficult to control using conventional methods and ideal arrangements remain unknown. Engineered polypeptides have emerged as powerful biomolecular tools in electrode assembly because binding sites and polypeptide structures can be easily modulated by changing the amino acid sequence. However, no studies have been conducted showing polypeptides can be engineered to interact with ionomers, attach them to metal surfaces, and control their arrangement. Our lab has recently developed this technology, using an elastin-like polypeptide to bind to metals, and bind to acidic and basic ionomer via ionic interactions. We use a quartz crystal microbalance with dissipation to provide detailed information about the loading, thickness, and binding behavior of the polypeptide and ionomer layers. We also use atomic force microscopy and grazing-incidence small-angle X-ray scattering to understand the impact of the biomolecules on ionomer phase separation. Finally, we have analyzed the performance (ionic conductivity) of the assembled films using interdigitated electrodes and electrochemical impedance spectroscopy. Through these techniques, we show that 1) our biomolecular system is highly flexible, easily adapting to different materials, 2) the polypeptide sequence can dictate ionomer phase separated structures, and 3) this system can be used to improve the performance of ionomer thin films and gain structure-function understanding. Generally, our results demonstrate that engineered polypeptides are promising tools for ionomer control in electrode engineering for fuel cells/electrolyzers and beyond. Furthermore, this work demonstrates that the creative combination of applied electrochemistry and biomolecular engineering supported and encouraged by leaders in each field can lead to unique research pathways that benefit heath, energy and the environment.