As a result of growing food demands, the area of land used globally for agriculture has rapidly increased over the last 300 years. Clearance of natural vegetation and conversion of land to agriculture is often associated with terrestrial carbon loss, from both vegetation and soil stores. Changes in terrestrial carbon storage has implications for food production, climate and water regulation. Quantifying these changes is therefore vital to understand the risks to and resilience of these benefits. Land use in the East of England has significantly changed during this period and is now predominantly used for agriculture, specifically arable use. In order to map changes to terrestrial carbon storage in this region since 1700, we apply a plant–soil system biogeochemistry model, N14CP. The model indicates carbon storage in the East of England has decreased by 109 Mt (−35.7%) during the study period, and whilst losses are observed in both soil and vegetation stores, vegetation losses as a result of forest clearance dominate. These findings have implications for carbon sequestration strategies; the largest carbon storage gains within the region are likely to be achieved through land-use transitions such as afforestation, rather than soil sequestration through changing arable management practices.