A sample preparation procedure for the analysis of tropane alkaloids (atropine and scopolamine) in multigrain cereal-based baby products (MGBP) has been optimized in this study. The protocol was based on a solid-liquid extraction, followed by purification by solid-phase extraction with MCM-41 functionalised with sulphonic acid groups as sorbent, before the analysis by ultra-performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry. The method was successfully validated with limits of quantification of 0.005 and 0.05 μg/kg for atropine and scopolamine, respectively. The analysis of a quality control material (TAs in baby food multigrain) demonstrated the suitability for the purpose of the methodology. The analysis of twenty commercial MGBP (mixtures of 2 to 10 cereal flours, with honey, milk, fruit pulp or juices) purchased between 2016 and 2024, revealed the presence of atropine (between 0.07 and 1.0 μg/kg) and scopolamine (between 0.15 and 12 μg/kg) in all the MGBP analysed.