Shifting cultivation systems of Southeast Asia are rapidly intensifying, especially through shortening of the fallow periods. It is typically assumed that intensification will result in a depletion of soil organic carbon (SOC) stocks, but existing estimates of carbon stocks in these systems are variable, and there is little certainty about the carbon outcomes of intensification. We investigated the effects of intensification on SOC stocks of a shifting cultivation system in northern Laos. Volume-specific soil samples were collected from 20 sites representing: i) various rotation intensities (fallow periods of 3–4 years and 7–10 years), ii) various stages of the rotation cycle (fallows and active fields) and iii) reference plots (old regrowth of 25–30 years). Samples were analyzed for SOC, soil texture, pH, Total Nitrogen and permanganate oxidizable carbon (POXC) – an active carbon fraction that has been suggested as an easily measured early indicator of land use induced changes in soil quality and SOC. There were no significant differences between SOC concentrations or stocks of any of the sites under shifting cultivation and the reference sites. However, the SOC stock under fallows in the intensive rotation category was significantly larger than the SOC stock under fallows in the extensive rotation category. This is likely because inputs of dead root biomass from the slashed vegetation provides an important input to the SOC pool. Fallow sites under intensive rotation had significantly higher contents of POXC in the topsoil than the active fields, which suggests that POXC captures the immediate effect of the decreased input of litter to the topsoil during the cultivation period. We conclude that in this study there is no evidence that intensification of shifting cultivation leads to a decline in total soil carbon stock, or to a decline in the more active carbon fraction measured by POXC. Therefore, narratives of shifting cultivation leading to a decline in soil carbon stocks need to be revisited, and land use policies related to the system should not uncritically be based on this incorrect assumption.