Weathering deterioration affects seed quality, especially in areas with excessive rainfall. This study aimed to evaluate the oxidative stress, physiological quality, and protein metabolism of seeds of different soybean cultivars under weathering deterioration at the pre-harvest phase. Six soybean cultivars (BMX Apolo, DM 6563, NS 5959, NA 5909, BMX Potência, and TMG 1175) were subjected to simulated rainfall at the R8 stage. Each level was divided into two applications at 72-h intervals: 60 mm (30 + 30), 120 mm (60 + 60), and 180 mm (90 + 90). Then, the seeds were harvested and evaluated for physiological potential, antioxidative enzymes, hydrogen peroxide, malondialdehyde, proteins, and protease activity. The simulated rainfall allowed the variation in seed moisture, promoting a significant reduction in germination and seed vigor, especially at 120 and 180 mm levels. There were also reductions in antioxidative enzyme activity with weathering deterioration (mainly for catalase, ascorbate peroxidase, and peroxidase), accumulation of hydrogen peroxide and malondialdehyde, and reductions in protein content and protease activity. The proposed rainfall system is efficient in inducing weathering deterioration during the pre-harvest phase and its deleterious effects. Weathering deterioration in soybean seeds in the pre-harvest stage is directly influenced by genotype.