Bacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells’ bioenergetic programming. Their role is thought to be linked to facilitating electron transfer between cells and the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure–function analysis of these structures within whole bacteria. In this work, we engineeredCupriavidus necatorH16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure–function relationships on conductivity and the effects this has on pili structure. This was achieved via a combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA™) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using aCupriavidus necatorchassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment.