This study investigated the physicochemical and phytochemical transformations occurring in Lepidium sativum L. seeds following an eight-day germination period. A comprehensive analysis was conducted on both non-germinated and germinated seeds, encompassing germination kinetics, physicochemical properties, particle size distribution, microstructure using scanning electron microscopy (SEM), Fourier-transform infrared (FTIR) spectroscopy, and gas chromatography-mass spectrometry (GC-MS). The results demonstrated a high germination rate and notable metabolic alterations during the germination process. The germinated seeds exhibited increased moisture content, acidity, and mineral levels, which were statistically significant (p < 0.05). Microscopic analysis revealed notable microstructural alterations, while FTIR confirmed modifications in functional groups, particularly an increase in the intensity of the O-H stretching band. Notably, GC-MS analysis demonstrated a substantial increase in linoleic acid within the lipid profile of germinated seeds. These findings underscore the considerable biochemical and structural changes induced by germination in L. sativum seeds and highlight their potential as a rich source of bioactive compounds for food and pharmaceutical applications.