With accelerating environmental change, understanding forest disturbance impacts on trade-offs between biodiversity and carbon dynamics is of high socio-economic importance. Most studies, however, have assessed immediate or short-term effects of disturbance, while long-term impacts remain poorly understood. Using a tree-ring-based approach, we analysed the effect of 250 years of disturbances on present-day biodiversity indicators and carbon dynamics in primary forests. Disturbance legacies spanning centuries shaped contemporary forest co-benefits and trade-offs, with contrasting, local-scale effects. Disturbances enhanced carbon sequestration, reaching maximum rates within a comparatively narrow post-disturbance window (up to 50 years). Concurrently, disturbance diminished aboveground carbon storage, which gradually returned to peak levels over centuries. Temporal patterns in biodiversity potential were bimodal; the first maximum coincided with the short-term post-disturbance carbon sequestration peak, and the second occurred during periods of maximum carbon storage in complex old-growth forest. Despite fluctuating local-scale trade-offs, forest biodiversity and carbon storage remained stable across the broader study region and our data support a positive relationship between carbon stocks and biodiversity potential. These findings underscore the interdependencies of forest processes, and highlight the necessity of large-scale conservation programs to effectively promote both biodiversity and long-term carbon storage, particularly given the accelerating global biodiversity and climate crises.