The objective was to analyze the influence of industrial soybean seed treatments on physiological quality throughout the storage and to evaluate the worth of the alcohol dehydrogenase (ADH) enzyme as a marker for quality monitoring. The statistical design used was completely randomized in a 2 × 5 × 5 factorial schemes involving two cultivars, five phytosanitary treatments, and five evaluation periods during storage. Before treatment, the lignin content of the seed coat of the cultivars was analyzed. The physiological quality was evaluated by the first count of germination and the germination, and the ADH enzyme was also quantified. The deterioration of soybean seeds during storage was directly linked to the type of molecule and the viscosity of the spray solution used in the treatment of seeds. The treatment of soybean seeds with predominantly aqueous solution and the use of systemic insecticidal molecules, combined with fungicides and polymers, impaired the germination of the stored seeds, and the deleterious effects became greater over time. ADH has potential as a marker of the physiological quality of treated and stored soybean seeds.