The growth of GaN nanowires having a polar, wurtzite structure on nonpolar Si substrates raises the issue of GaN nanowire polarity. Depending on the growth procedure, coexistence of nanowires with different polarities inside one ensemble has been reported. Since polarity affects the optical and electronic properties of nanowires, reliable methods for its control are needed. In this work, we use Kelvin probe force microscopy to assess the polarity of GaN nanowires grown by plasma-assisted Molecular Beam Epitaxy on Si(111) substrates. We show that uniformity of the polarity of GaN nanowires critically depends on substrate processing prior to the growth. Nearly 18% of nanowires with reversed polarity (i.e., Ga-polar) were found on the HF-etched substrates with hydrogen surface passivation. Alternative Si substrate treatment steps (RCA etching, Ga-triggered deoxidation) were tested. However, the best results, i.e., purely N-polar ensemble of nanowires, were obtained on Si wafers thermally deoxidized in the growth chamber at ~1000 °C. Interestingly, no mixed polarity was found for GaN nanowires grown under similar conditions on Si(111) substrates with a thin AlOy buffer layer. Our results show that reversal of nanowires’ polarity can be prevented by growing them on a chemically uniform substrate surface, in our case on clean, in situ formed SiNx or ex situ deposited AlOy buffers.