Patterning the electronic properties of semiconducting polymers on surfaces at the nanometer scale has a significant impact on their application in nanophotonics and nanoelectronics. Surprisingly, little attention has been paid to methods employing the phase transition from crystal to melt and thermally activated oxidation of conjugated polymer crystals, both accompanied by dramatic changes in electrical conductivity. Here, we propose a novel concept based on bias-controlled scanning probe lithography (SPL) which permits localized oxidation of poly(3-hexylthiophene) (P3HT) crystals and enables the on-demand formation of nanoscale, nonconductive structures without visible changes in topography. The approach relies on Joule heating induced local melting and oxidation of P3HT, resulting in nanoscopic nonconductive structures. Besides locally switching off electrical conductivity, this approach even allows to tune the electrical conductivity by adjusting the applied bias. Thus, we can generate patterns with nanometer spatial resolution and controllable conductivity within crystals of conjugated polymer through bias-controlled physical and chemical changes of the polymer.