In this work, Hexagonal Mesoporous Silica (HMS) and Santa Barbara Amorphous-15 (SBA-15) mesostructured silicas were synthesized and functionalized with sulfonic acid groups. The materials (HMS-SO3− and SBA-15-SO3−) were evaluated as strong cation exchange sorbents for sample extract clean-up, by solid phase extraction (SPE) and dispersive solid phase extraction, to determine atropine (At) and scopolamine (Sc) in commercial culinary aromatic herbs. Under optimized conditions, 0.25 g of sample was subject to solid–liquid extraction with acidified water (pH 1.0), and good recovery percentages were achieved for At and Sc using 75 mg of HMS-SO3− in SPE as the clean-up stage, prior to their determination by HPLC-MS/MS. The proposed method was validated in a thyme sample showing recoveries in the range of 70–92%, good linearity (R2 > 0.999), adequate precision (RSD ≤ 14%) and low limits (MDL 0.8–2.2 µg/kg and MQL 2.6–7.2 µg/kg for both analytes). Sixteen aromatic herbs samples (dried thyme, basil and coriander leaves) were analysed and At was found in fourteen samples over an interval of <5–42 μg/kg, whereas Sc was found in three of the sixteen samples studied (between <5–34 μg/kg). The amount of At and Sc found in some analysed samples confirms the importance of setting maximum levels of At and Sc in culinary aromatic herbs.