This study examines the occurrence of psychoactive opium and tropane alkaloids in ceramic vessels from the Funnel Beaker Culture (FBC) using optimized GC-MS/MS and LC-MS/MS analytical protocols. Twelve vessels and potsherds, including miniature forms and collared flasks, were subjected to standardized extraction, derivatization, and chromatographic analysis. The GC-MS/MS method enabled highly sensitive detection of target compounds (LOD < 0.5 ng/g), while LC-MS/MS provided complementary confirmation of analytes. Papaverine was identified in three artifacts (N1, N2, G2) using GC-MS/MS, and its presence was independently confirmed in two of these vessels (N1, N2) by LC-MS/MS. In one miniature vessel (D1), trace amounts of tropane alkaloids—scopolamine and presumptive atropine—were detected following derivatization. Recovery values ranged from 55% to 61%, demonstrating effective alkaloid isolation despite extensive degradation processes and strong interactions between organic residues and the ceramic matrix. The analytical results indicate that psychoactive plant derivatives could have been intentionally used and stored in selected FBC vessels, supporting interpretations related to ritual or medicinal practices. The validated procedures developed in this work provide a robust framework for the detection of unstable biomolecular residues in prehistoric ceramics and can be applied to future archaeometric and materials-science research. Keywords: GC-MS/MS; LS-MS/MS; Funnel Beaker Culture; vessels; pottery; psychoactive substances; opium; tropane; alkaloids