The post-harvest process at the storage stage is one of the most critical processes for maintaining soybean seed quality. The type of packaging and the type of material stored will affect its shelf life. One type of packaging has specific properties that are different from other types of packaging. Therefore, this study used several types of packaging materials and soybean varieties to determine changes in its quality during storage. The treatments were arranged in a 5 × 4 × 7 factorial experiment in a randomised block design (RBD) with three replications, consisting of totally 140 treatment combinations involving five different types of packaging materials. Water content, the weight of 100 grains, seedling dry weight, electrical conductivity (EC), and germination percentage were assessed monthly. The factorial analysis of variance (ANOVA) was used to compare water content, the weight of 100 grains, EC, germination, and seedling dry weight. A qualitative descriptive analysis method was employed for the temperature and relative humidity of the storage room. The results showed that Grobogan had the lowest germination percentage of 84.85% compared to the other varieties (86.97–90.82%). Plastic sack resulted in the most inferior seed quality (82.00% for plastic sack vs. 88.23–90.17% for the other containers). A more extended storage period of soybean seeds caused a decrease in soybean quality for all varieties and packaging materials. Up to 6 months of storage at room temperature, the quality of soybean seeds remained high, with the lowest germination of 80%.