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Semi-arid and arid ecosystems dominated by shrubs (“dry shrublands”) are an important component of the global C cycle, but impacts of climate change and elevated atmospheric CO2 on biogeochemical cycling in these ecosystems have not been synthetically assessed. This study synthesizes data from manipulative studies and from studies contrasting ecosystem processes in different vegetation microsites (that is, shrub or herbaceous canopy versus intercanopy microsites), to assess how changes in climate and atmospheric CO2 affect biogeochemical cycles by altering plant and microbial physiology and ecosystem structure. Further, we explore how ecosystem structure impacts on biogeochemical cycles differ across a climate gradient. We found that: (1) our ability to project ecological responses to changes in climate and atmospheric CO2 is limited by a dearth of manipulative studies, and by a lack of measurements in those studies that can explain biogeochemical changes, (2) changes in ecosystem structure will impact biogeochemical cycling, with decreasing pools and fluxes of C and N if vegetation canopy microsites were to decline, and (3) differences in biogeochemical cycling between microsites are predictable with a simple aridity index (MAP/MAT), where the relative difference in pools and fluxes of C and N between vegetation canopy and intercanopy microsites is positively correlated with aridity. We conclude that if climate change alters ecosystem structure, it will strongly impact biogeochemical cycles, with increasing aridity leading to greater heterogeneity in biogeochemical cycling among microsites. Additional long-term manipulative experiments situated across dry shrublands are required to better predict climate change impacts on biogeochemical cycling in deserts.