The anodic oxidation of niobium is investigated in pure molten ortho-phosphoric acid (o-H3PO4). At applied potentials in the 2.5–60 V range and for electrolyte temperatures in the 60–110 °C range, porous niobium oxide layers are formed. Pore ordering and morphology depend on the anodization voltage, time and temperature, i.e. the anodic oxide develops different morphologies depending on low- or high-field anodizing conditions. At 100 °C and low voltages, e.g. ≤ 5 V, vertically oriented, amorphous oxide nanopores with cylindrical shape (“nanochannels”) grow with an average diameter of 5–8 nm. Higher voltages (10–20 V) lead to a less ordered pore morphology, resembling a “fish bone” structure. At 40–60 V, and after a sufficiently long anodization time (≥30 min), an orthorhombic Nb2O5 hierarchical structure forms that shows a bimodal pore size distribution with some 100 nm wide main pores that branch out into ∼ 10 nm wide side nanochannels. A partial crystallization of the anodic oxide is observed at high voltages (≥40 V). We propose that this is due to a high field-induced crystallite nucleation in the barrier oxide at the oxide/metal interface. With time, the crystalline oxide is incorporated in the porous layer. The main pores, partially crystalline and hence more stable in the anodizing electrolyte, result from the gradual dissolution of the amorphous side nanochannels.