The material of storage containers affects the shelf life and the chemical composition of food. Artisanal agave spirits, such as mezcal and bacanora, might be filled into low-cost plastic bottles that compromise product quality. We developed an analytical platform to identify the bottle materials of agave spirits, which employs 3D-printed cartridges, and the robotic platform Open LabBot/Open SprayBot for paper-spray ionization mass spectrometry (PS-MS). The bottle material of 102 fresh samples could be identified with a 2 % error. Samples stored for two years at −20 °C in glass vials still were classified correctly in 76 % of the cases. Therefore, the spirits still appear adulterated for a prolonged time after re-bottling into inert containers. The measurement time is about 30 s/sample. Thus, the 3D-PS-MS strategy can be applied for the high-throughput screening for bottle materials of agave spirits and other alcoholic beverages.