Atmospheric [CO₂] is rising, with significant consequences for plant function in natural and managed ecosystems. Currently we cannot fully explain the effects of elevated [CO₂] on vegetation under field conditions, where interactions with abiotic and biotic factors are important. To better understand plant responses to elevated [CO₂] we have combined genomic, biochemical, physiological and ecological investigation of soybean grown in the field at the SOYbean Free-Air Concentration Enrichment (SOYFACE) facility at the University of Illinois. Soybean was grown in four plots at ambient [CO₂] (~380 ppm) and four plots at elevated [CO₂] (~550 ppm), from sowing until harvest. This provided a model system, where low genetic and environmental variability between experimental units increased the ability to detect subtle treatment effects. The impact of elevated [CO₂] on dark respiration is a controversial subject, with prior studies variously reporting stimulation, inhibition or no change in CO₂ efflux. The principal molecular response of soybean to elevated [CO₂] was increased gene expression for many components of respiratory metabolism, including glycolysis, the TCA cycle and mitochondrial electron transport. These molecular responses were reflected in greater pool sizes of key carbon metabolites and greater rates of respiratory oxygen uptake and carbon efflux. The integrated genomic, biochemical and physiological responses provide unique evidence for stimulated respiration at elevated [CO₂]. Greater respiration will partially offset the stimulation of photosynthesis by elevated [CO₂] at whole-plant and ecosystem scales, while also generating additional energy and carbon-skeletons. Gene expression for some associated biosynthetic pathways was altered. Gene expression for cellulose synthesis was greater at elevated [CO₂], but gene expression for lignin synthesis did not change. Greater cellulose to lignin ratios can alter the rate of leaf litter decomposition. In summary, microarray analysis revealed previously unknown changes in gene expression which underlie key physiological and ecological responses of soybean to elevated [CO₂].