Despite their prevalence, little attention has been given to quantifying arid land soil and ecosystem carbon fluxes over prolonged, annually occurring dry periods. We measured soil [CO2] profiles and fluxes (Fs) along with volumetric soil moisture and temperature in bare interplant canopy soils and in soils under plant canopies over a three-month hot and dry period in a Chihuahuan Desert shrubland. Nocturnal Fs was frequently negative (from the atmosphere into the soil), a form of inorganic carbon exchange infrequently observed in other deserts. Negative Fs depended on air-soil temperature gradients and were more frequent and stronger in intercanopy soils. Daily integrated ecosystem-level Fs was always positive despite lower daily Fs in intercanopy soils due to nocturnal uptake and more limited positive response to isolated rains. Subsurface [CO2] profiles associated with negative Fs indicated that sustained carbonate dissolution lowered shallow-soil [CO2] below atmospheric levels. In the morning, positive surface Fs started earlier and increased faster than shallow-soil Fs, which was bidirectional, with upward flux toward the surface and downward flux into deeper soils. These dynamics are consistent with carbonate precipitation in conjunction with convection-assisted CO2 outgassing from warming air and soil temperatures and produced a pronounced diurnal Fs temperature hysteresis. We concluded that abiotic nocturnal soil CO2 uptake, through a small carbon sink, modulates dry season ecosystem-level carbon dynamics. Moreover, these abiotic carbon dynamics may be affected by future higher atmospheric carbon dioxide levels and predictions of more prolonged and regular hot and dry periods.