Reduced grain and seed nutrient content in crops grown under elevated CO2 concentrations (eCO2) have raised concerns about future food security. Studies have reported that different seed elements responded differently to eCO2. Additionally, the nutrient response to eCO2 varied across species and cultivars. This study investigated the response of seed quality in two soybean cultivars (HS93‐4118 and Loda) previously shown to have different yield responses to eCO2. We show that seed quality responded differently to eCO2 for the two cultivars and that elements were differentially impacted. The strongest declines under eCO2 were observed for Al, Ca, Fe, and Se while P and Mn were unaffected. Seed protein content increased under eCO2 for the two cultivars. Oil content, however, showed a negative relationship with yield and declined under eCO2. Using path analysis, we show that eCO2 reduced the seed content for some elements through increasing seed yield, effectively diluting the elemental concentrations, while other elements were reduced in a yield‐independent manner. Despite the decline in the seed concentration for some elements, the overall yield per hectare of elements, protein, and oil under eCO2 increased because of greater seed yield. We quantified the economic impact of altered seed composition and show that the decline in oil content with increasing soybean yield at eCO2 could adversely impact profits.