In this study we combine spectroscopic data (diffuse reflectance infrared Fourier transform spectroscopy, DRIFTS, and X-ray photoelectron spectroscopy, XPS) with ab initio SCF calculations on model systems in order to get insight into the short-range order of amorphous aluminophosphate oxynitride (AlPON) catalysts. The use of fixed P/Al = 1/1 atomic ratio and varying N/O atomic ratio in the models, allowed us to consider stoichiometries with nitrogen contents in the range 0-20 wt %, similar to those found experimentally. The observed trends in computed Koopman ionization potentials (IPs), vibrational frequencies, and thermodynamic stability are compared with experimental XPS and DRIFTS data and available information of aluminophosphate and related systems. They are used to propose a structural model for the short-range structure of amorphous aluminophosphate oxynitrides. From the XPS data it can be concluded that first nitrogen enters the phosphorus coordination sphere; this results in the formation step by step of [PO3N] and [PO2N2] polyhedra that coexist with [PO4] ones, their relative proportion depending on the total nitrogen content of the sample. On the basis of both experimental and ab initio SCF calculations, it can be concluded that the amorphous solids are formed by P-X-P (X = O, N) rings connected to each other by aluminum atoms. On the basis of the thermodynamic stability of the different bonds, nitrogen enters preferentially the phosphorus coordination sphere.