Vertically aligned Nb2O5 nanochannel layers are grown on Nb metal substrates by self-organizing electrochemical anodization in a pure molten o-H3PO4 electrolyte. The capacitive behavior of these structures when used as negative electrodes is investigated in aqueous 1 M Na2SO4 electrolyte, in a potential range from −0.2 to −1.25 V vs. SCE. Surface chemistry, morphology and crystallographic features of the Nb2O5 nanochannel electrodes are tailored by adjusting the synthesis parameters, namely anodization time and crystallization temperature, which have a significant effect on the electrode performance. 8 μm thick Nb2O5 nanochannel layers that are converted into orthorhombic phase by crystallization at 450 °C, display a maximized areal capacitance of ∼100 mF cm-2 at a current density of 1 mA cm−2. These electrodes retain 63% of the initial capacitance at 10 mA cm−2 and 81% after 1500 charge-discharge cycles at a current density of 1.3 mA cm−2. Kinetic analysis of the electrochemical results reveals the occurrence of pseudocapacitive and diffusion-controlled processes. Electrochemical impedance spectroscopy evidences for these structures a low resistance across the electrode and at the electrode/substrate interface. These results are associated with the nanochannel morphology (high active area) of the Nb2O5 layers, and are ascribed to their crystalline nature, which provides an “oriented porosity” for ion diffusion and directional pathways for charge transport and collection.