The combination of amino acids anions with a choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a combined experimental and theoretical study of a choline–proline ionic liquid, using both large and small angle X-ray diffraction (WAXS–SAXS), and classical and ab initio molecular dynamics calculations, in which we are able to point out for the first time the existence of a low Q peak in the X-ray patterns in the absence of linear or branched alkyl chains. From the calculations, we can obtain theoretical scattering patterns that reproduce very nicely the experimental spectra in all Q ranges, and from detailed analysis of the radial distribution functions (RDFs) and hydrogen bond patterns, we can state that very strong ion pairs are established in the liquid and the observed pre-peak can be ascribed to the interactions between atoms belonging to different ion pairs.