Carbon cycling associated with biological soil crusts, which occupy interspaces between vascular plants in drylands globally, may be an important part of the coupled climate-carbon cycle of the Earth system. A major challenge to understanding CO₂ fluxes in these systems is that much of the biotic and biogeochemical activity occurs in the upper few mm of the soil surface layer (i.e., the ‘mantle of fertility’), which exhibits highly dynamic and difficult to measure temperature and moisture fluctuations. Here, we report a multi-sensor approach to simultaneously measuring temperature and moisture of this biocrust surface layer (0–2 mm), and the deeper soil profile, concurrent with automated measurement of surface soil CO₂effluxes. Our results illuminate robust relationships between biocrust water content and field CO₂ pulses that have previously been difficult to detect and explain. All observed CO₂ pulses over the measurement period corresponded to surface wetting events, including when the wetting events did not penetrate into the soil below the biocrust layer (0–2 mm). The variability of temperature and moisture of the biocrust surface layer was much greater than even in the 0–5 cm layer of the soil beneath the biocrust, or deeper in the soil profile. We therefore suggest that coupling surface measurements of biocrust moisture and temperature to automated CO₂flux measurements may greatly improve our understanding of the climatic sensitivity of carbon cycling in biocrusted interspaces in our study region, and that this method may be globally relevant and applicable.