Peatlands are a significant global carbon (C) store, which can be compromised by drainage and afforestation. Quantifying the rate of C loss from peat soils under forestry is challenging, as soil CO2 efflux includes both CO2 produced from heterotrophic peat decomposition and CO2 produced by tree roots and associated fungal networks (autotrophic respiration). We experimentally terminated autotrophic below-ground respiration in replicated forest plots by cutting through all living tree roots (trenching) and measured soil surface CO2 flux, litter input, litter decay rate, and soil temperature and moisture over 2 years. Decomposition of cut roots was measured and CO2 fluxes were corrected for this, which resulted in a large change in the fraction heterotrophic : autotrophic flux, suggesting that even 2 years after trenching decaying root biomass makes significant contributions to the CO2 flux. Annual peat decomposition (heterotrophic CO2 flux) was 115 ± 16 g C m−2 yr−1, representing ca. 40 % of total soil respiration. Decomposition of needle litter is accelerated in the presence of an active rhizosphere, indicating a priming effect by labile C inputs from roots. This suggests that our estimates of peat mineralization in our trenched plots are conservative and underestimate overall rates of peat C loss. Considering also input of litter from trees, our results indicate that the soils in these 30-year-old drained and afforested peatlands are a net sink for C, since substantially more C enters the soil organic matter than is decomposed heterotrophically. This study does not account for fluvial C fluxes, which represent a small flux compared to the CO2 soil efflux; further, root litter and exudate deposition could be a significant C source that is only partially sampled by our approach, adding to these plantations being a potential carbon sink. However, the C balance for these soils should be taken over the lifespan of the trees, in order to determine if the soils under these drained and afforested peatlands are a sustained sink of C or become a net source over longer periods of forestry.