This protocol describes the digestion process of mollusc larvae and is modified from the procedure found in Becker et al. (2005). Here, we indicate the entire process to obtain the digestion solution, as well as cleaning glassware, actual larval digestion and extraction of shells until storage for subsequent geochemical analysis or observation. This protocol is applicable to shelly larvae of any species, once they are collected and brought to the laboratory. The goal of this preparation is to isolate each larval shell to perform individual geochemical analyses, instead of dissolving several specimens for bulk analysis. To do this, great care needs to be taken to the handling of the shells using ultra-pure solutions and acid-washed glassware to avoid chemical contamination of all kind. Reference: Becker, B.J., Fodrie, F.J., McMillan, P.A., Levin, L.A., 2005. Spatial and temporal variation in trace elemental fingerprints of mytilid mussel shells: a precursor to invertebrate larval tracking. Limnology and Oceanography, 50, 48-61. doi: 10.4319/lo.2005.50.1.0048.