The spectroscopy technique of Micro-Raman is an appropriate method to investigate the microscopic structure of internally heterogeneous (i.e., composed of multiple layers) agro-food products. The effects of applying magnetic fields (magneto-priming technique) and imbibition on the chemical makeup of Triticale seed were studied, particularly in its pericarp, germ and endosperm parts, with the help of Micro-Raman. In light of the results obtained, the magneto-primed seeds soaked in water presented a greater number of chemical compounds than the control seeds, although those treatments were not as effective as the ones with only magneto-priming. The effects of the magneto-priming treatment were especially noticeable in the endosperm due to the large number of chemical compounds identified. The seed composition differences among treatments showed that the use of Micro-Raman jointly with magneto-priming is an appropriate method to obtain and analyse information of the key components of Triticale seeds, notably regarding their pericarp and endosperm.