We present and discuss the role of nanoparticles size and stoichiometry over the local atomic environment of nanostructured VOx films. The samples have been characterized in situ using X-ray absorption near-edge structure (XANES) spectroscopy identifying the stoichiometry-dependent fingerprints of disordered atomic arrangement. In vanadium oxides, the ligand atoms arrange according to a distorted octahedral geometry depending on the oxidation state, e.g. trigonal distortion in V2O3 and tetragonal distortion in bulk VO2. We demonstrate, taking VO2 as a case study, that as a consequence of the nanometric size of the nanoparticles, the original ligands symmetry of the bulk is broken resulting in the coexistence of a continuum of distorted atomic conformations. The resulting modulation of the electronic structure of the nanostructured VOx as a function of the oxygen content reveals a stoichiometry-dependent increase of disorder in the ligands matrix. This work shows the possibility to produce VOx nanostructured films accessing new disordered phases and provides a unique tool to investigate the complex matter.