A substantial carbon (C) debt has been accrued due to long-term cropping for global food production emitting carbon dioxide from soil. However, the factors regulating the persistence of soil organic C (SOC) remain unclear, with this hindering our ability to develop effective land management strategies to sequester organic C in soil. Using a Ferralsol from semi-arid subtropical Australia, alteration of bulk C contents and fractions due to long-term land use change (up to 72 years) was examined with a focus on understanding whether SOC lost due to cropping could be restored by subsequent conversion back to pasture or plantation. It was found that use of soil from cropping for 72 years resulted in the loss of >70 % of both C and N contents. Although conversion of cropped soil to pasture or plantation for up to 39 years resulted in an increase in both C and N, the C contents of all soil fractions were not restored to the original values observed under remnant vegetation. The loss of C with cropping was most pronounced from the particulate organic matter fraction, whilst in contrast, the portion of the C that bound strongly to the soil mineral particles (i.e. the mineral-associated fraction) was most resilient. Indeed, aliphatic C was enriched in the fine fraction of mineral-associated organic matter (<53 m). Our findings were further confirmed using Synchrotron-based micro-spectroscopic analyses of intact microaggregates, which highlighted that binding of C to soil mineral particles is critical to SOC persistence in disturbed soil. The results of the present study extend our conceptual understanding of C dynamics and behaviour at the fine scale where C is stabilized and accrued, but it is clear that restoring C in soils in semi-arid landscapes of subtropical regions poses a challenge.