Earthworms co-determine whether soil, as the largest terrestrial carbon reservoir, acts as source or sink for photosynthetically fixed CO₂. However, conclusive evidence for their role in stabilising or destabilising soil carbon has not been fully established. Here, we demonstrate that earthworms function like biochemical reactors by converting labile plant compounds into microbial necromass in stabilised carbon pools without altering bulk measures, such as the total carbon content. We show that much of this microbial carbon is not associated with mineral surfaces and emphasise the functional importance of particulate organic matter for long-term carbon sequestration. Our findings suggest that while earthworms do not necessarily affect soil organic carbon stocks, they do increase the resilience of soil carbon to natural and anthropogenic disturbances. Our results have implications for climate change mitigation and challenge the assumption that mineral-associated organic matter is the only relevant pool for soil carbon sequestration.