In Switzerland, over 90 % of peatlands have been degraded and transitioned from long-term carbon sinks to persistent carbon sources. Assessing peat carbon vulnerability and restoration opportunities requires understanding not only the present-day distribution of peat carbon stocks, but also the historical trajectories that shaped them. Existing assessments are largely based on inventories and emission-factor approaches, limited in representation of the interactive effects of climate, peatland processes, and land-use change over time. By combining the LPX-Bern Dynamic Global Vegetation Model with a historical record-informed peat-derived area and carbon accounting framework, we reconstructed peatland conversion pathways and tracked the fate of peat carbon through successive land-use transitions from the pre-industrial period to the present. Modelled peatland and peat-derived areas in Switzerland declined from approximately 724 km² in the pre-industrial period (1701–1710) to 376 km² at present (2011–2020), while only 5 % remained near-natural, in broad agreement with historical reconstructions and recent synthesis products. Over the same period, peat carbon stocks decreased from 121.9 Mt C under near-natural conditions to 30.4–56.4 Mt C. Although only a small fraction of the original peatlands remained near-natural, 86–92 % of the remaining peat carbon was stored in agricultural, forested, and unmanaged drained land-cover classes. By explicitly tracking peat carbon through historical land-use transitions and attributing remaining peat carbon to present-day land-cover classes, this framework provides a spatially explicit basis for assessing peat carbon vulnerability, identifying restoration opportunities, and informing peatland management and climate mitigation strategies. This approach is transferable to other regions where information on peatland extent, land-use history, and peat-specific disturbances is available.