The structural stability of some nanostructured titanates was investigated in terms of their subsequent processing and possible applications. With the aim to investigate their mechanochemical stability, we applied high-energy ball milling and studied the resulting induced phase transitions. Hydrogen titanates with two different morphologies, microcrystals and nanotubes, were taken into consideration. The phase-transition sequence was studied by Raman spectroscopy and X-ray powder diffraction, while the morphology and crystal structure, on the nanoscale, were analyzed by high-resolution transmission electron microscopy. During the mechanochemical treatment of both morphologies, the phase transitions from hydrogen titanate to TiO2 anatase and subsequently to TiO2 rutile were observed. In the case of hydrogen trititanate crystals, the phase transition to anatase starts after a longer milling time than in the case of the titanate nanotubes, which is explained by the larger particle size of the crystalline powder. However, the phase transition from anatase to rutile occurred more quickly in the crystalline powder than in the case of the nanotubes.