Human and natural disturbances are key drivers of change in forest ecosystems. Yet, the direct and indirect mechanisms which underpin these changes remain poorly understood at the ecosystem level. Here, using structural equation modelling across a 150+ year chronosequence, we disentangle the direct and indirect effects of major disturbances in a temperate forest ecosystem. We show that wildfires, logging and post-fire (salvage) logging can affect plant and microbial communities and abiotic soil properties both directly and indirectly through plant–soil–microbial interactions. We quantified 68 direct and indirect disturbance effects across these components, with the majority resulting in ecosystem-wide adverse effects. Indirect disturbance effects accounted for 43% of total disturbance effects, with some amplifying or partially mitigating direct disturbance effects. Overall, human disturbances were associated with more negative effects than natural disturbances. Our analyses provide novel insights into the multifaceted dynamics of forest disturbances and the mechanisms which underpin their relative impacts.