The exact chemical structure of non-crystallising natural products is still one of the main challenges in Natural Sciences. Despite tremendous advances in total synthesis, the absolute structural determination of a myriad of natural products with very sensitive chemical functionalities remains undone. Here, we show that a metal-organic framework (MOF) with alcohol-containing arms and adsorbed water, enables selective hydrolysis of glycosyl bonds, supramolecular order with the so-formed chiral fragments and absolute determination of the organic structure by single-crystal X-ray crystallography in a single operation. This combined strategy based on a biomimetic, cheap, robust and multigram available solid catalyst opens the door to determine the absolute configuration of ketal compounds regardless degradation sensitiveness, and also to design extremely-mild metal-free solid-catalysed processes without formal acid protons.