Seed quality is a limiting factor in the search for high soybean yields. However, fungi and insect pests can negatively interfere with their performance, and industrial seed treatment (IST) is a tool used to minimize the attack of pathogens and pests. The treated seeds are often stored until sowing, which can lead to a reduction in their quality. This work aimed to evaluate the physical and physiological quality of soybean seeds submitted to IST, with subsequent storage in a natural and controlled environment. The experiment was conducted in a split-split-plot design in a completely randomized scheme (time x storage systems x IST) with four replications. Soybean cultivar 55I57RSF IPRO was subjected to IST with fungicide (metalaxyl-M, thiabendazole, and fludioxonil) and insecticide (thiamethoxam and cyantraniliprole), combined or not with polymer and dry powder, with subsequent storage in a controlled and natural environment. The moisture content, thousand-seed weights, germination, first germination count, germination speed index, accelerated aging, seedling length, dry matter transfer, and emergence sand test were evaluated. IST did not affect the moisture content and weight of a thousand seeds. However, storage in a controlled environment provided a greater reduction in moisture content and a smaller reduction in the weight of a thousand seeds. IST negatively affected germination, first germination count, germination speed index, and accelerated aging test. IST negatively affected plant length, except in the treatment where only insecticide was applied. The dry mass transfer was negatively affected but with less intensity in seeds subjected only to the application of insecticide or fungicide and the combination of insecticide, fungicide, and polymer. Seed emergence in the sand was negatively affected by all treatments. Regardless of the treatments, all responses evaluated showed a reduction throughout storage, with greater intensity in seeds stored in the natural environment.