This work presents a detailed investigation of the preparation of MoVTeNbOx catalysts by hydrothermal synthesis. Phase-pure synthesis of M1 has been achieved applying the metals in a molar ratio Mo/V/Te/Nb = 1/0.25/0.23/0.12. Raman, UV/Vis spectroscopy, and SEM/EDX analysis show that the elements are inhomogeneously distributed in the initial suspension that is formed after mixing the metal salts in an aqueous medium. Iso- and heteropoly anions of molybdenum, free telluric acid as well as supra-molecular polyoxometalate clusters are observed in the solution, whereas all metals have been found in the precipitate. Complete rearrangement of molecular building blocks under hydrothermal conditions is essential for formation of phase-pure materials. Optimized synthesis conditions with respect to temperature and time result in the formation of a precursor consisting of nano-structured M1 characterized by an extended periodic organization in the [001] direction and a fairly homogeneous distribution of the elements. Residual ammonium containing supra-molecular species in the precursor result in the formation of phase mixtures during the subsequent crystallization by heat treatment in inert gas. Phase-pure M1 exhibits a distinct degree of flexibility with respect to the chemical composition that becomes obvious by incorporating Nb not exclusively into pentagonal bi-pyramidal units, but also into octahedral coordinated positions as shown by EXAFS. Anisotropic growth of the needle-like M1 crystals has been observed during the final heat treatment performed at 873–923 K in inert atmosphere disclosing a potential method to control the catalytic properties of MoVTeNbOx catalysts.