Variations in geochemical signatures of fossil brachiopod shells may be due to diagenesis and/or biological processes (i.e. ‘vital effects’). Characterize them is crucial to identify reliable areas into the shell suitable to paleoclimatological studies. This investigation contributes to an in-depth understanding of geochemical variations of Gigantoproductus sp. shells (SW Spain, Serpukhovian age), which could affect to the Late Paleozoic Ice Age interpretation. Microstructural, crystallographic, cathodoluminescence and geochemical (minor and trace elements, δ18O, δ13C, and strontium isotopes) characterisation have been performed on the tertiary layer of the ventral valve, to assess the preservation state. Poorly-preserved areas exhibit microstructural and geochemical changes such as recrystallisation, fracturing and higher Mn and Fe enrichment. Moreover, these areas have higher dispersion of ⁸⁶Sr, ⁸⁷Sr, δ18O and δ13C than well-preserved areas. Three structural regions have been identified in well-preserved areas of ventral valve by differences in valve curvature and thickness, such as the umbonal, thick and thin regions. These regions have different proportions of Mg, S, Na, δ18O, and δ13C, whom are interpreted as ‘vital effects’ and probably are related with growth rate differences during shell growth. Gigantoproductus tertiary layer seems the best suitable to paleoclimatological studies because it retains the original microstructure and geochemistry.