Land use change in the rangelands of Botswana is affecting soil properties. Pastoralism is the only viable livelihood for many rural poor in Botswana, and privatization of communal land is reducing the area of grazing available to those without land tenure. This has elevated stocking densities in communal areas, increasing pressure on soils and vegetation. Field experiments were used to quantify the impact of grazing intensity on soil organic carbon (SOC) and CO2 efflux on biologically crusted aridisols in the SW Kalahari. Differences in soil properties under an encroaching shrub species, under trees and in open-grass sites were also determined. Soil CO2 efflux was significantly higher and SOC significantly lower on soils for 2 years after intense grazing disturbance compared to control soils. In contrast, light grazing disturbance resulted in an increase in chlorophyll a and SOC but no change in soil CO2 efflux. Total C and N concentrations and soil CO2 efflux were significantly greater in soils under shrubs and trees compared to grass sites. The microclimate was also different, with higher summer temperatures but lower winter temperatures at the grass sites compared to shrubs. Shading under vegetation canopies significantly reduced solar radiation reaching the soil surface. The findings demonstrate the importance of biological soil crusts (BSCs) to SOC and that intensive grazing, which destroys crusts through trampling and burial, adversely affects C sequestration and storage. Grazing management which results in less frequent and intense disturbance to the soil surface could benefit SOC stores by maintaining a healthy BSC cover. However, simplistic notions of reducing cattle numbers or implementing rotational grazing regimes in communal rangeland are problematic given the much wider significance of cattle ownership to pastoral communities.