Advancing soft electronics requires a nascent class of filler that exhibits high conductivity yet remains chemically and mechanically compatible with the host matrix. Conductive protein nanowires or pili function as the conducting element of protein-based soft electronics. Molecular simulations with coarse-grained models will survey the interplay of pili amino acid sequences and exposed surface peptide residues with soft materials chemistry to create a data-rich system that establishes foundational design principles for pili fillers in soft polymer matrices. The inherent aqueous dispersion properties of conductive pili enable the design, characterization, and production of both bulk pili-polymer nanocomposites and electrospun pili-polymer nanofiber mats with well-distributed filler. Advanced electron and scanning probe microscopy will interrogate the structural and electronic properties of the pili and provide a feedback loop that refines the molecular models. Directed agglomeration of pili into bundles and electrospun pili-elastomer fibers will also enable studies on the scalability of this new nanocomposite platform. Molecular models will ultimately unveil surface peptide sequences that improve processability and functionality of new pili strains and pili-polymer nanocomposites that are validated by rheology, microscopy, transport, and tensile testing methods.