Land use change is causing substantial loss of soil organic carbon (SOC). However, little is known regarding how this loss of SOC influences the composition of carbon (C) functional groups and their microscale distribution, with this being critical to the protection and storage of SOC. In this study, we examined the mechanisms influencing preservation of C forms and their distribution by comparing soils under native vegetation and cropping at two Australian sites, Waco black Vertisol (70 y cropping) and Langlands-Logie grey Vertisol (10 y cropping). Land use change caused the loss of up to 23 % (5.3 mg C g<sup>-1</sup> soil) of bulk SOC. Strikingly, the greatest loss occurred in the mineral-associated organic carbon (MAOC) fraction that accounted for 72–91 % of total SOC. Interestingly, despite losing up to 23 % of the bulk SOC, the C that remained after long-term cropping was similar in speciation to that in the native soils revealed by near edge X-ray absorption fine structure spectroscopy. In a similar manner, the use of infrared microspectroscopy showed that the forms of C remained similar in the two land uses and that C was closely associated with clay minerals. This suggests that the SOC loss from mineral fraction was not due to preferential consumption of particular forms of carbon, but rather, an overall loss of SOC in the mineral fractions and an increase in overall lability. These observations provide critical evidence that preservation of SOC is not driven by increasing compositional diversity or complexity in these Vertisols and that physical protection of C is of importance. Potential exists to rebuild SOC in the mineral-associated fraction under cropping. Management practices should promote the building of organo-mineral associations.