In this work, we use 3D-ED to solve the previously unknown crystal structure of synthetic xanthine from a single submicron-sized particle found in a commercial powder sample. This result demonstrates the potential of the technique for structure elucidation of scarce biogenic xanthine samples to advance exploration in the field of organic biomineralisation. In addition, we show that the quality of the electron diffraction data is sufficient to refine hydrogen atom positions using kinematical 3D-ED techniques.