It has been suggested that desert vegetation will show the strongest response to rising atmospheric carbon dioxide due to strong water limitations in these systems that may be ameliorated by both photosynthetic enhancements and reductions in stomatal conductance. Here, we report the long-term effect of 55 Pa atmospheric CO2 on photosynthesis and stomatal conductance for three Mojave Desert shrubs of differing leaf phenology (Ambrosia dumosa—drought-deciduous, Krameria erecta—winter-deciduous, Larrea tridentata—evergreen). The shrubs were growing in an undisturbed ecosystem fumigated using FACE technology and were measured over a four-year period that included both above and below-average precipitation. Daily integrated photosynthesis (Aday) was significantly enhanced by elevated CO2 for all three species, although Krameria erecta showed the greatest enhancements (63% vs. 32% for the other species) enhancements were constant throughout the entire measurement period. Only one species, Larrea tridentata, decreased stomatal conductance by 25–50% in response to elevated CO2, and then only at the onset of the summer dry season and following late summer convective precipitation. Similarly, reductions in the maximum carboxylation rate of Rubisco were limited to Larrea during spring. These results suggest that the elevated CO2 response of desert vegetation is a function of complex interactions between species functional types and prevailing environmental conditions. Elevated CO2 did not extend the active growing season into the summer dry season because of overall negligible stomatal conductance responses that did not result in significant water conservation. Overall, we expect the greatest response of desert vegetation during years with above-average precipitation when the active growing season is not limited to ∼2 months and, consequently, the effects of increased photosynthesis can accumulate over a biologically significant time period.