Preservation of arthropod cuticles is of paramount importance for taphonomic interpretations in which the fossil record of the chitin-protein complex is considered a key molecular signature of the group studied. In this work, different specimens of clam shrimps and their surrounding sedimentary matrix recovered from four localities of the La Matilde Formation (Patagonia, Argentina) were chemically analyzed for the first time by Laser-induced breakdown spectroscopy (LIBS) and RAMAN spectroscopic techniques. The spectral data recorded from the fossils were processed and analyzed through multivariate statistics, including Principal Component Analysis (PCA), Nonmetric Multidimensional Scaling (NMDS), and Analysis of Similarities (ANOSIM). The correlation between the different colorations featured by the specimens and the atomic chemical composition of their carapaces was systematically investigated to gain a better understanding of the fossilization processes together with more detailed interpretations. We found that the carapaces featuring a yellow-brown color exhibited a similar chemical profile with iron predominance, while those with the same color as the sedimentary matrix presented a distinctive composition. Considering the volcanic influence to which the different localities studied and carapaces were exposed, we propose that the clam shrimps from the four localities were preserved in at least three ways, namely, (1) pyritization; (2) admixed preservation; and (3) impression, each with distinctive characteristics of the taphonomic processes involved. Overall, results obtained provide useful information to achieve a more comprehensive knowledge about the taphonomy of fossils in a Jurassic lacustrine paleo-environment, as the La Matilde Formation.