Abstract The objective of this work was to analyze structurally the pods and seed coats of soybean (Glycine max) cultivars, as well as to determine the quality of seeds when subjected to deterioration by weathering in pre-harvest. A 7×3 factorial arrangement was used – seven cultivars and three volumes of simulated rainfall (0, 54, and 162 mm). Exposure to rainfall was simulated in the R8 phenological stage. Then, the plants were taken to a greenhouse, where they were kept until the time of collection of pods and seeds. After collection, the following evaluations were carried out: tetrazolium test, lignin content in pods and seed coats, and structural analysis of pods (exocarp, mesocarp, and endocarp thickness) and seed coats (epidermis, hypodermis, and parenchymal-cell thickness). Pre-harvest rainfall of 54 and 162 mm reduces the quality of soybean seeds; however, the response to deterioration by weathering differs according to the cultivar. The tolerance to all simulated rainfall was greater for BRSMT Pintado, BRS Jiripoca, and M8210IPRO and lower for BRS 1010IPRO. Pods with a greater thickness of the exocarp, mesocarp, and endocarp and a high lignin content show greater resistance to weathering deterioration and seeds with greater vigor and viability. The thickness of the hypodermis of the testa is related to resistance to weathering deterioration and to the obtainment of high-quality seeds.