Net productivity of vegetation is determined by the product of the efficiencies with which it intercepts light (ɛi) and converts that intercepted energy into biomass (ɛc). Elevated carbon dioxide (CO2) increases photosynthesis and leaf area index (LAI) of soybeans and thus may increase ɛi and ɛc; elevated O3 may have the opposite effect. Knowing if elevated CO2 and O3 differentially affect physiological more than structural components of the ecosystem may reveal how these elements of global change will ultimately alter productivity. The effects of elevated CO2 and O3 on an intact soybean ecosystem were examined with Soybean Free Air Concentration Enrichment (SoyFACE) technology where large field plots (20-m diameter) were exposed to elevated CO2 (∼550 μmol mol−1) and elevated O3 (1.2 × ambient) in a factorial design. Aboveground biomass, LAI and light interception were measured during the growing seasons of 2002, 2003 and 2004 to calculate ɛi and ɛc. A 15% increase in yield (averaged over 3 years) under elevated CO2 was caused primarily by a 12% stimulation in ɛc , as ɛi increased by only 3%. Though accelerated canopy senescence under elevated O3 caused a 3% decrease in ɛi, the primary effect of O3 on biomass was through an 11% reduction in ɛc. When CO2 and O3 were elevated in combination, CO2 partially reduced the negative effects of elevated O3. Knowing that changes in productivity in elevated CO2 and O3 were influenced strongly by the efficiency of conversion of light energy into energy in plant biomass will aid in optimizing soybean yields in the future. Future modeling efforts that rely on ɛc for calculating regional and global plant productivity will need to accommodate the effects of global change on this important ecosystem attribute.