Global economic change and policy interventions are driving transitions from long-fallow swidden (LFS) systems to alternative land uses in Southeast Asia’s uplands. This study presents a systematic review of how these transitions impact upon livelihoods and ecosystem services in the region. Over 17 000 studies published between 1950 and 2015 were narrowed, based on relevance and quality, to 93 studies for further analysis. Our analysis of land-use transitions from swidden to intensified cropping systems showed several outcomes: more households had increased overall income, but these benefits came at significant cost such as reductions of customary practice, socio-economic wellbeing, livelihood options, and staple yields. Examining the effects of transitions on soil properties revealed negative impacts on soil organic carbon, cation-exchange capacity, and aboveground carbon. Taken together, the proximate and underlying drivers of the transitions from LFS to alternative land uses, especially intensified perennial and annual cash cropping, led to significant declines in pre-existing livelihood security and the ecosystem services supporting this security. Our results suggest that policies imposing land-use transitions on upland farmers so as to improve livelihoods and environments have been misguided; in the context of varied land uses, swidden agriculture can support livelihoods and ecosystem services that will help buffer the impacts of climate change in Southeast Asia.