This work presents an optimized methodology based on the miniaturization of the original QuEChERS (μ-QuEChERS) followed by liquid chromatography coupled to mass spectrometry (HPLC-MS/MS) for the determination of tropane alkaloids (TAs), atropine, and scopolamine in leafy vegetable samples. The analytical methodology was successfully validated, demonstrating quantitation limits (MQL) ≤2.3 ng/g, good accuracy, and precision, with recoveries between 90–100% and RSD ≤ 13% for both analytes. The method was applied to the analysis of TA-producing plants (Brugmansia versicolor, Solandra maxima, and Convolvulus arvensis). High concentrations of scopolamine were found in flowers (1771 mg/kg) and leaves (297 mg/kg) of B. versicolor. The highest concentration of atropine was found in flowers of S. maxima (10.4 mg/kg). Commercial mixed leafy vegetables contaminated with B. versicolor and S. maxima were analysed to verify the efficacy of the method, showing recoveries between 82 and 110% for both analytes. Finally, the method was applied to the analysis of eighteen samples of leafy vegetables, finding atropine in three samples of mixed leafy vegetables, with concentrations of 2.7, 3.2, and 3.4 ng/g, and in nine samples with concentrations ≤MQL. In turn, scopolamine was only found in a sample of chopped Swiss chard with a concentration ≤MQL.