Developing methodologies employed to trace the geographic origin of seafood as accurate and fast as possible can help to speed-up the delivery of results to legal authorities, reduce associated costs and minimize environmental impacts (associated with the residues generated). The present study evaluated if trace element fingerprints (TEF) of a small homogenized subsample of Manila clams (Ruditapes philippinarum) right valve yielded a representative elemental signature of the whole shell. Four elemental ratios (Ba/Ca, Mg/Ca, Mn/Ca and Sr/Ca) commonly employed to trace the geographic origin of bivalves were determined from subsamples of 0.2 and 3 g of the homogenized right valve and the whole left valve (4 g). A Canonical Analysis of Principal Coordinates developed for the subsamples of small portions (0.2 g) of the homogenized right valve revealed an accuracy of 100%, that led to the correct classification of the subsample of 3 g to their respective valve and that of 4 g to its matching shell. Results achieved indicate that TEF of a small homogenized portion of a bivalves valve is representative of the whole shell and can be employed to provide an accurate, fast, reliable and environmentally safer method to trace its geographic origin. •Trace element fingerprints can be used to trace the geographic origin of bivalves.•A small portion of one valve can be used as a reliable proxy of the whole shell.•This approach makes ICP-MS analysis more environmentally friendly.•This approach is faster and equally reliable for traceability of geographic origin.