The chemical treatment of corn seeds is widely adopted for protecting crops at the early stages. However, some molecules interfere in the quality of seeds, especially when stored, by accelerating their deterioration. The objective of this work was to investigate the influence of insecticides on the enzymatic expression and quality of corn seeds subjected to storage. Seeds of the hybrids 2B647PW and SHS4070 were subjected to four different chemical treatments (standard treatment, standard + clothianidin, standard + thiamethoxam, and standard + fipronil) and stored for different periods (0, 3, 6, and 9 months). The quality evaluation included the germination test, first germination count, cold test, and health test. The expression of the enzymes α-amylase, esterase, superoxide dismutase, catalase, and alcohol dehydrogenase were determined by the gel electrophoresis technique. The insecticides clothianidin, thiamethoxam, and fipronil reduce the physiological quality of the seeds of hybrid 2B647PW after nine months of storage. The treatment of seeds with the insecticides clothianidin, thiamethoxam, and fipronil reduces the expression of α-amylase, superoxide dismutase, and catalase enzymes after nine months of storage. The enzymes α-amylase, superoxide dismutase, catalase, and alcohol dehydrogenase are good quality markers for hybrid corn seeds.