Soybean seed tends to lose its quality property if kept in inappropriate storage conditions. The aim of this work was to evaluate the effect of different oxygen (O2) and carbon dioxide (CO2) partial pressures, combined with different temperatures on the soybean seed physiological potential maintenance. In 2017, seed of the cultivars 8473 RSF and TECIRGA 6070RR were stored for 7 months under: [1] ambient air; controlled atmosphere (CA) with [2] 1 kPa O2 + 0.04 kPa CO2; [3] 2 kPa O2 + 0.04 kPa CO2; [4] 2 kPa O2 + 30 kPa CO2; and [5] 2 kPa O2 + 80 kPa CO2. In 2018, seed of NA 5909 RG and FEPAGRO 37RR were stored for 7 months under the following conditions: [1] ambient air; and CA with [2] 1 kPa O2 + 0.04 kPa CO2; [3] 1 kPa O2 + 15 kPa CO2; [4] 1 kPa O2 + 30 kPa CO2; [5] 2 kPa O2 + 0.04 kPa CO2. In both years the storage conditions were conducted at three temperatures (20, 25 and 30 °C). The seed were stored with moisture content between 11 and 11.5. The reduction of the O2 until 1.0 kPa maintained higher germination, however, storage above 25 °C is not recommended. High CO2 partial pressure did not have additional effects on physiological quality conservation compared to solely low O2. Seed of 8473 RSF stored at 25 and 30 °C resulted in low germination, regardless of the CA condition. NA 5909 RG reached 80% of germination, when CA was used, regardless of temperature. The ambient air did not maintain the seed physiological quality when stored at 25 and 30 °C and CA may efficiently maintain the physiological quality of soybean seed after 7 months, even in the higher temperature for NA5909 RG, but not for the other cultivars.