The stratigraphic classification and correlation of Permian-Lower Triassic clastic beds in the Central European Basin System traditionally rely on geophysical, bio-, and lithostratigraphic methods. However, in basin margin areas, the accuracy of these tools is diminished due to the heterogeneous distribution of stratigraphic markers, lack of index fossils, and greater climatic and tectonic disturbance. To overcome these limitations, this study introduces a more versatile, multifaceted and chemostratigraphy-based approach. By integrating results from bulk X-ray fluorescence analysis, sandstone petrography, Raman heavy mineral analysis, lithofacies characterisation and borehole gamma-ray logs, we produce robust multi-stratigraphic schemes for selected sequences in the Franconian Basin (SE Central European Basin System). Hierarchical chemostratigraphic zones, comprising five chemozones and sixteen subzones, were designed using key elemental ratios (Ga/Rb, Rb/K, Na/K, Ca/Mg, Cr/Ti, Th/Ti, Nb/Th, Ti/Nb, P/Ti, Zr/P, Zr/Y), whose changes through time reflect modifications in the mineralogical composition of sedimentary rocks. To ensure precise interpretations of geochemical data, we established links between mineralogical and chemical components through statistical processing and direct comparison with mineralogical assemblages. Our results demonstrate that chemostratigraphic boundaries can identify major changes in palaeo-depositional environments and sediment sources induced by eustatic, tectonic and climatic disturbances. For example, changes in the P/Ti and Zr/P ratios across the CP3-CT1 document the increased abundance in apatite-rich granitic detritus, resulting from the exposure of new source lithologies in the catchment area due to Early Triassic synsedimentary tectonism. Since these perturbations had a regional impact on sedimentation, their geochemical fingerprints are correlated across the basin, regardless of lithofacies variability or distance between sections. Moreover, integrating characteristic geochemical signals into multi-stratigraphic schemes enables more precise placement of stratigraphic boundaries, identification of locally deposited/preserved stratigraphic markers, and overall refinement of outdated classification schemes. The chemostratigraphic approach introduced in this study offers a solution to the limitations of conventional stratigraphic tools, allowing robust characterisations and correlations of Permian-Triassic sequences in the marginal regions of the Central European Basin System. In addition, the multi-analytical workflow for processing geochemical data, refining stratigraphic schemes and attributing geochemical anomalies to environmental perturbations represents a further step towards more precise applications of chemostratigraphy to the depositional record.