Sepia eumelanin, a natural biopigment extracted from cuttlefish ink, has attracted growing interest as a sustainable material for organic electronics. Its nanogranular structure, composed of DHI and DHICA monomers, presents unique charge transport characteristics influenced by hydration and measurement scale. While prior studies have explored its mixed ionic–electronic conductivity at micro- and millimetric ranges, the intrinsic electronic properties at the nanoscale remain underexplored. In this study, we investigate the nanoscale charge transport behavior of Sepia melanin using e-beam lithography-fabricated electrodes with submicron separations. Through current–voltage, current–time, and electrochemical impedance spectroscopy measurements, we observed predominantly electronic transport mechanisms, with conductivity increasing at smaller interelectrode distances. Temperature-dependent analysis enabled extraction of activation energy values, further elucidating the transport processes. These findings underscore the relevance of distance scale in assessing the true conductive potential of natural materials and support Sepia melanin’s viability in bio-inspired electronic applications.