The study of the conducting-probe atomic force microscopy (AFM) ambient-air nanopatterning of a molecular conducting single crystal is reported. The implication of electrochemical reactions both in the substrate modification, which yield nanometer-scale insulating regions, and in the conducting-probe-mediated complementary water redox reaction is demonstrated. The rate of the process controlling the dimension of the resulting insulating regions is mainly controlled by the conducting-probe potential. The faradaic currents are found to be exceedingly low as compared to the total current flowing in the AFM probe contact-junction and a proposed model validates this feature.