Transition to organic farming requires the development of new methods to protect seeds from adverse factors. The germinative process and the post-germinative phase are strictly controlled by the oxidative balance involving lipid peroxidation, reactive oxygen species and enzymes activity, directing the plant viability and its further development. We focus our studies mainly on the seeds protection and fortification through natural solutions based on marigold and fenugreek extracts, steroid alkaloids from tomatoes and hydrolyzed proteins derived from leather waste industry. The structural configuration of the plant protection products proves significant effects fighting on different mechanisms of seeds’ oxidative stress. As well as the experimental design highlighted a tandem correlative mechanism between germination, decrease of lipid peroxidase and activation of catalase and superoxide-dismutase. SEM-PROTECT II was the most active biopesticide involved in these processes. Our findings directed complex research oriented to technological and experimental optimizations for the development of an innovative, efficient and competitive plant protection product to meet modern agriculture requirement.