Cold plasma has been used to promote seed germination. In this study, soybean seeds were directly treated with cold plasma (CP) for different durations (0, 30, 60, 120, and 180 s) and then cultivated with cold-plasma-activated water (PAW) during germination. The effects of CP and PAW treatment on the physical–biochemical properties and nutritional components of soybean sprouts were investigated. The results showed that sprout length increased by 41.07% after moderate CP (60 s) and further increased with PAW. The fresh weight increased by 11.24% after moderate CP treatment. Although sugar content decreased with CP, it increased with PAW. Total amino acid and isoflavone content increased after moderate CP treatment. Both CP and PAW treatments increased the intercellular water and weakened the fluidity of water, and small-molecule proteins were polymerized into large-molecule proteins. The solubility of protein was enhanced under PAW treatment. However, neither PAW nor CP treatment exerted a significant influence on the secondary structure of proteins. The hardness of the soybean sprouts decreased and their fracturability increased after moderate CP treatment. This study demonstrates that cold plasma has the potential to enhance the biomass and edible quality of soybean sprouts.