We analyse the electrical and optical properties of single GaN nanowire p-n junctions grown by plasma-assisted molecular-beam epitaxy using magnesium and silicon as doping sources. Different junction architectures having either a n-base or a p-base structure are compared using optical and electrical analyses. Electron-beam induced current (EBIC) microscopy of the nanowires shows that in the case of a n-base p-n junction the parasitic radial growth enhanced by the magnesium (Mg) doping leads to a mixed axial-radial behaviour with strong wire-to-wire fluctuations of the junction position and shape. By reverting the doping order p-base p-n junctions with a purely axial well-defined structure and a low wire-to-wire dispersion are achieved. The good optical quality of the top n nanowire segment grown on a p-doped stem is preserved. A hole concentration in the p-doped segment exceeding 1018 cm-3 was extracted from EBIC mapping and photoluminescence analyses. This high concentration is reached without degrading the nanowire morphology.