Amorphous formulations are increasingly used in the pharmaceutical industry due to their increased solubility, but their structural characterization at atomic-level resolution remains extremely challenging. Here, we characterize the complete atomic-level structure of an amorphous glucagon-like peptide-1 receptor (GLP-1R) agonist using chemical shift driven NMR crystallography. The structure is determined from measured chemical shift distributions for 17 of the 32 carbon atoms and 16 of the 31 hydrogen atoms in the molecule. The chemical shifts are able to provide a detailed picture of the atomic-level conformations and interactions, and we identify the structural motifs that play a major role in stabilization of the amorphous form. In particular, hydrogen bonding of the carboxylic acid proton is strongly promoted, although no carboxylic acid dimer is formed. Two orientations of the benzodioxole ring are promoted in the NMR structure, corresponding to a significant stabilization mechanism. Our observation that inclusion of water leads to stabilization of the carboxylic acid group might be used as a strategy in future formulations where hydrogen bonding between neighboring molecules may otherwise be hindered by sterics.