A novel method was developed and applied to the determination of the most representative tropane alkaloids (TAs), atropine and scopolamine, in gluten-free (GF) grains and flours by HPLC-MS/MS. Accordingly a suitable sample treatment procedure based on solid-liquid extraction (SLE) and followed by strong cation-exchange solid-phase extraction (SCX-SPE) was optimized. SBA-15 mesostructured silica functionalized with sulfonic acids was evaluated as sorbent. The proposed method was fully validated in sorghum flour showing good accuracy with recoveries in the range of 93–105%, good linearity (R2 > 0.999) and adequate precision (RSD < 20%). Low method quantification limits (MQL) were obtained (1.5 and 2.4 µg/kg for atropine and scopolamine, respectively) and no matrix effect was observed thanks to the extraction and clean-up protocol applied. The method was applied to 15 types of GF samples of pseudocereals (buckwheat, quinoa and amaranth), cereals (teff, corn and blue corn, sorghum and millet) and legumes (red and green lentil, chickpea and pea). Atropine was found above the MQL in eight of them, with values between 7 and 78 µg/kg, while scopolamine was only found in teff flour, its concentration being 28 µg/kg. The method developed is an interesting tool for determining TAs in a variety of samples of GF grains and flours. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.