There are three main components of soybean (Glycine max (L.) Merr.) seeds: protein, oil, and residual. The residual fraction includes soluble and insoluble carbohydrates, lignin, and minerals. Among soluble carbohydrates, the presence of raffinose family of oligosaccharides (RFOs) has poor nutritional value (i.e., raffinose and stachyose), and the inability of monogastric animals to digest them limits the potential use of soybean meal for food and feed applications. Our objective was to understand how different environmental conditions impact soybean seed quality, particularly the concentration of the residual fraction and its components. Nine commercial genotypes from three maturity groups were sown on early and late dates. The concentration of insoluble carbohydrates + lignin was positively associated with seed weight (r = 0.67) and negatively associated with the mean temperature during the seed‐filling period (R5–R7; r = −0.61). Within soluble carbohydrates, RFOs were negatively influenced by the mean temperature at the beginning of the seed‐filling period (R5–R6; r = −0.37), while sucrose concentration showed the opposite effect (r = 0.43). In contrast, precipitation exhibited a positive correlation with RFOs, whereas sucrose displayed a negative correlation (r = 0.38 and r = −0.42). This study showed that the decrease in protein concentration was related to the increase in the residual fraction of the seeds, and higher temperatures during seed‐filling period impacted the residual composition of the seeds, specifically by reducing RFO concentration.