The aim of this study was to evaluate the isoenzyme activity in soybean seeds with different lignin contents subjected to harvest delay with artificial incidence of rainfall before and after storage. The experiment was conducted in a randomized block design with three replicates and a 5 × 3 × 2 factorial design, being five soybean cultivars, three harvest seasons (R8, R8 + one pre-harvest rainfall simulation, and R8 + two pre-harvest rainfall simulations), and two storage seasons (0 and 180 days). The pre-harvest rainfall simulations were performed through irrigation at the intensity of 30 mm of water until the pods were soaked and then collected after reached 18% water content. Seeds were evaluated regarding chemical composition (lignin content), physiological quality (germination, accelerated aging), and enzymatic activity (catalase, esterase, alcohol dehydrogenase, malate dehydrogenase, and isocitratelyase). The cultivar AS 7307 RR showed higher lignin content in the integument and higher physiological quality. The harvest delay and the artificial incidence of rainfallpromotesvariation in the electrophoretic pattern of the enzymes catalase, esterase, alcohol dehydrogenase; malate dehydrogenase, and isocitratelyase for stored and non-stored seeds.