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Because industrial agriculture keeps expanding in Southeast Asia at the expense of natural forests and traditional swidden systems, comparing biodiversity and ecosystem services in the traditional forest–swidden agriculture system vs. monocultures is needed to guide decision making on land-use planning. Focusing on tree diversity, soil erosion control, and climate change mitigation through carbon storage, we surveyed vegetation and monitored soil loss in various land-use areas in a northern Bornean agricultural landscape shaped by swidden agriculture, rubber tapping, and logging, where various levels and types of disturbance have created a fine mosaic of vegetation from food crop fields to natural forest. Tree species diversity and ecosystem service production were highest in natural forests. Logged-over forests produced services similar to those of natural forests. Land uses related to the swidden agriculture system largely outperformed oil palm or rubber monocultures in terms of tree species diversity and service production. Natural and logged-over forests should be maintained or managed as integral parts of the swidden system, and landscape multifunctionality should be sustained. Because natural forests host a unique diversity of trees and produce high levels of ecosystem services, targeting carbon stock protection, e.g. through financial mechanisms such as Reducing Emissions from Deforestation and Forest Degradation (REDD+), will synergistically provide benefits for biodiversity and a wide range of other services. However, the way such mechanisms could benefit communities must be carefully evaluated to counter the high opportunity cost of conversion to monocultures that might generate greater income, but would be detrimental to the production of multiple ecosystem services.