Physical fractions of soil organic matter (SOM) are established indicators of management-induced change and have been used to estimate the soil carbon storage capacity and storage potential. Here, we use SOM physical fractions and soil textures to identify management practices that maintain or enhance soil health and carbon storage in agricultural soils in Ontario. Metadata from the National Soil Database were used to estimate carbon storage potentials and calculate carbon deficits. A map was created showing carbon deficits in Ontario's agricultural soils and indicates that these soils have the potential to store an additional 0 to 2kgm⁻² in the top 20cm of the soil. Tillage system generally had no effect on the size of the carbon deficit at four long-term agricultural experiments (Delhi, Elora, Ottawa, and Ridgetown). There was only a significant tillage effect at Ridgetown and only in the maize–soybean crop rotation, where the carbon deficit was 2.95gCkgsoil⁻¹ under conventional tillage compared to 8.97gCkgsoil⁻¹ with no tillage. A statistically significant effect of crop rotation was detected in Elora and Ridgetown. In Elora, continuous alfalfa had the smallest carbon deficit (7.25gCkgsoil⁻¹) and maize–soybean rotation had the largest deficit (12.07gCkgsoil⁻¹). In Ridgetown, the maize–soybean rotation had the smallest carbon deficit (2.95gCkgsoil⁻¹). Regression analysis showed a weak negative relationship (R²=0.11; P<0.001) between carbon storage deficits and soil health scores. This suggests that increasing SOM levels alone may not improve soil health.