Fossil carbonate skeletons of marine organisms are archives for understanding the development and evolution of palaeo-environments. However, the correct assessment of past environment dynamics is only possible when pristine skeletons and their biogenic characteristics are unequivocally distinguishable from diagenetically-alteredskeletal elements and non-biogenic features. In this study, we extend our work on diagenesis of biogenic aragonite (Casella et al. 2017) to the investigation of biogenic low-Mg calcite using brachiopod shells. We examined and compared microstructural characteristics inducedby laboratory-based alteration to structural features derived from diagenetic alteration in natural environments. We used four screening methods: cathodoluminescence (CL), cryogenic and conventional field emission-scanning electronmicroscopy (FE-SEM), atomic force microscopy (AFM) and electron backscatter diffraction (EBSD).We base our assessments of diagenetic alteration and overprint on measurements of, a) images of optical overprint signals, b) changes in calcite crystal orientation patterns, and c) crystal co-orientation statistics. According to the screening process, altered and overprinted samples define two groups. In Group 1 the entire shell is diagenetically overprinted, whereas in Group 2 the shell contains pristine as well as overprinted parts. In the case of Group 2 shells, alteration occurred either along the periphery of the shell including the primary layer or at the interior-facing surface of the fibrous/columnar layer. In addition, we observed an important mode of the overprinting process, namely the migration of diagenetic fluids through the endopunctae corroborated by mineral formation and overprinting in their immediate vicinity, while leaving shell parts between endopunctae in pristine condition. Luminescence (CL) and microstructural imaging (FE-SEM) screening give first-order observations of the degree of overprint as they cover macro-to micron scale alteration features. For a comprehensive assessment of diagenetic overprint these screening methods should be complemented by screening techniques such as EBSD and AFM. They visualise diagenetic changes at submicron and nanoscale levels depicting the replacement of pristine nanocomposite mesocrystal biocarbonate (NMB) by inorganic rhombohedral calcite (IRC). The integration of screening methods allows for the unequivocal identification of highly-detailed alteration features as well as an assessment of the degree of diagenetic alteration.