Geochemical markers are being increasingly applied to fundamental questions in population and community ecology in marine habitats because they allow inferences on individuals dispersal, but vital effects, small sample size and instrumental limitation are still challenging particularly in deep-sea studies. Here we use shells of the deep-sea bivalve Idas modiolaeformis to assess potential effects of sample storage, mineralogy, and valve orientation on LA-ICPMS measurements. Trace element concentrations of 24Mg, 43Ca, 88Sr, 137Ba, 208Pb, and 238U are not affected by the two most commonly used storage methods of biologic deep-sea samples (frozen at –20°C and fixed in 95% ethanol); thus combined analysis of differently preserved specimens is possible when the number of individuals is insufficient and distinct sample fixation is needed for multiple purposes. Valve orientation had a strong impact on quantification of trace elements in the calcitic but not in the aragonitic layer of adult shells. Hence, to enable comparisons between adult shells and entirely aragonitic embryonic shells, a reference map of site-specific signatures can potentially be generated using the aragonitic layer of the adult shells. Understanding ontogenetic changes and environmental effects in trace element incorporation is critical before geochemical fingerprinting can be used as a tool for larval dispersal studies in the deep-sea.