Savanna regions are increasingly developed for agriculture to support population growth, food demand and export economies. This is driving interest in the conversion of natural savanna to cattle grazed pastures or horticultural crops in Northern Australia. Savanna clearing leads to aboveground carbon (C) loss but impacts below-ground are less certain as studies have focused on high rainfall regions, low reactive clay soils and shallow depths of 0.3 m or less. To examine impact of land use change (LUC) in Northern Australia, we sampled the upper 1.0 m soil profile of: 1) savanna woodlands, 2) old and young C4 perennial cattle grazed pastures and 3) old and young, melon-sorghum rotation fields. Soil C concentrations and soil bulk density in the upper 0.3 m were significantly greater in cattle grazed pastures than savanna woodland, such that savanna to pasture LUC significantly increased soil C density from 30.2 ± 1.5–43.4 ± 3.0 Mg C ha-1 over 28 years. Soil bulk density in the upper 0.7 m of savanna woodland was significantly less than that in the melon-sorghum rotations. In contrast, soil C concentrations below 0.5 m were significantly greater in the savanna woodland than in the 3 y.o. melon-sorghum rotation fields. There was no significant difference in soil C density between savanna woodland and 12 y.o. melon-sorghum rotations. This may relate to the beneficial effects of ploughing in sorghum as a green manure, or simply that the decrease in soil C concentration was offset by increased soil C density in the upper layers of soil where most C is located. In contrast, conversion of savanna to cattle grazed pasture sites is equivalent to a soil sequestration rate of 0.34 Mg C ha-1 y-1, approximately 50% of the observed net ecosystem productivity estimated using eddy covariance methods. Changing the depth to which soil C density was estimated changed significant differences amongst land-use systems. Whereas, estimating soil C density using a ‘fixed depth’ or ‘equivalent mass’ method did not change the statistical significance. There is an increasing focus on the potential of soil carbon sequestration especially in north Australia and understanding potential change and impact of accounting methods is essential for meaningful policy development. Policy settings to maintain, or improve, soil C storage and soil health may contradict agricultural development goals.