Northern peatlands store ~30% of the world’s soil carbon. This carbon sequestration is due to slow decomposition, as illustrated by ancient wooden artefacts and ‘bog bodies’ preserved over millennia. Such artefacts suggest that carbon could be captured externally and stored long term in peat. However, whether such carbon would remain stable following lowered water tables is not known. Here, we show that adding woody litter results in preservation of the exogenous carbon, as well as protection of soil carbon within the host ecosystem from severe drought, as a result of leached polyphenolics. These compounds not only inhibit microbial extracellular and intracellular metabolism but also deprive microbial growth of iron and substrates such as carbon and nitrogen. Our results suggest that this technique harnesses natural ecosystem resilience mechanisms and may have implications for new carbon-farming approaches.