For the development and application of GaN-based nanowire structures, it is crucial to understand their fundamental properties. In this work, we provide the nano-scale correlation of the morphological, electrical, and optical properties of GaN/AlGaN nanowire light emitting diodes (LEDs), observed using a combination of spatially and spectrally resolved cathodoluminescence spectroscopy and imaging, electron beam-induced current microscopy, the nano-probe technique, and scanning electron microscopy. To complement the results, the photo- and electro-luminescence were also studied. The interpretation of the experimental data was supported by the results of numerical simulations of the electronic band structure. We characterized two types of nanowire LEDs grown in one process, which exhibit top facets of different shapes and, as we proved, have opposite growth polarities. We show that switching the polarity of nanowires (NWs) from the N- to Ga-face has a significant impact on their optical and electrical properties. In particular, cathodoluminescence studies revealed quantum wells emissions at about 3.5 eV, which were much brighter in Ga-polar NWs than in N-polar NWs. Moreover, the electron beam-induced current mapping proved that the p–n junctions were not active in N-polar NWs. Our results clearly indicate that intentional polarity inversion between the n- and p-type parts of NWs is a potential path towards the development of efficient nanoLED NW structures.