Multiwalled vanadium oxide nanotubes are an intriguing class of materials due to their complex and functional structure. They have especially gained attention as an electrode material for rechargeable ion batteries exhibiting Li-ion storage capacities up to 250 mAh/g. The pristine nanotube materials and their electrochemical properties have previously been investigated extensively; however little knowledge exists on the structural transformations induced by ion storage in vanadium oxide nanotube electrodes. In this work, the changes in the atomic-scale and nanoscale structure during lithium- and magnesium-ion storage in two types of vanadium oxide nanotubes are investigated by operando powder X-ray diffraction and total X-ray scattering. Linear expansion and contraction of the VOx layers with vanadium reduction and oxidation are observed, while the interlayer spacing is found to be drastically dependent on the nature of the templating molecules or ions residing in the interlayer space of the pristine tubes. The study demonstrates how certain conditions will lead to destruction of the multilayer structure of the tubes, while leaving the individual VOx layers intact. Pair distribution function analysis reveals that vanadium reduction induces a change in the vanadium coordination geometry in the VOx layers from square pyramidal to octahedral.