Biological soil crusts (biocrusts) are predicted to be sensitive to the increased temperature and altered precipitation associated with climate change. We assessed the effects of these factors on soil carbon dioxide (CO₂) balance in biocrusted soils using a sequence of manipulations over a 9-year period. We warmed biocrusted soils by 2 and, later, by 4°C to better capture updated forecasts of future temperature at a site on the Colorado Plateau, USA. We also watered soils to alter monsoon-season precipitation amount and frequency and had plots that received both warming and altered precipitation treatments. Within treatment plots, we used 20 automated flux chambers to monitor net soil exchange (NSE) of CO₂ hourly, first in 2006–2007 and then again in 2013–2014, for a total of 39 months. Net CO₂ efflux from biocrusted soils in the warming treatment increased a year after the experiment began (2006–2007). However, after 9 years and even greater warming (4°C), results were more mixed, with a reversal of the increase in 2013 (i.e., controls showed higher net CO₂ efflux than treatment plots) and with similarly high rates in all treatments during 2014, a wet year. Over the longer term, we saw evidence of reduced photosynthetic capacity of the biocrusts in response to both the temperature and altered precipitation treatments. Patterns in biocrusted soil CO₂ exchange under experimentally altered climate suggest that (1) warming stimulation of CO₂ efflux was diminished later in the experiment, even in the face of greater warming; and (2) treatment effects on CO₂ flux patterns were likely driven by changes in biocrust species composition and by changes in root respiration due to vascular plant responses.