Food fraud is perpetrated with increasing frequency along the food chain, triggering the need for new and modern tools to detect food authenticity. Chia, flax and sesame seeds are well known for the good nutritional characteristics of their oils, but there is a lack of knowledge regarding the authenticity of these seeds and food products containing them as well. In the present work, we propose a method based on targeted metabolomics to identify the polyphenols present in seeds, which can be used as markers of authenticity. We tentatively identified 44 polyphenols in the different seeds by HPLC-DAD-ESI-qTOF (MS/MS). Chemometrics allowed the selection of 12 compounds, which are nominated as novel markers for seed authentication. Some of these compounds were also found in a lab-scale preparation of cookies supplemented with the studied seeds. The proposed chemical markers resisted the baking process, representing good candidates to be used in the authentication of raw material and bakery products containing these seeds.