The Soybean Free Air Concentration Enrichment (SoyFACE) facility began in 2001 to investigate the response of the soybean agro-ecosystem to increasing atmospheric carbon dioxide and ozone concentrations. Elevated CO2 concentration (550 ppm) increased soybean agronomic yield by approximately 15%. Variation in yield response of cultivars was not associated with variation in leaf-level photosynthetic capacity; however, there was significant variation in investment in antioxidant capacity in soybean cultivars. A multi-year genomic and physiological study revealed that greater respiratory capacity of soybean grown at elevated [CO2] was driven by greater abundance of transcripts encoding enzymes throughout the respiratory pathway, which would be needed for the greater number of mitochondria. Greater respiratory quotient and leaf carbohydrate content at elevated [CO2] provided evidence that stimulated respiration was supported by the additional photoassimilate available from enhanced photosynthesis at elevated [CO2]. The greater respiratory capacity also provided fuel for stimulated growth of soybean leaves at elevated [CO2]. Altered soybean leaf and canopy properties had important ecological consequences, such as altering herbivore feeding patterns and earthworm burrowing habits, which influences soil properties and resource availability.