Measures of particulate organic carbon (POC), humus organic carbon (HOC), and resistant organic carbon (ROC) (primarily char) are often used to represent the active, slow, and inert carbon pools used in soil carbon models. However, these fractions are difficult to measure directly, and mid infrared (MIR) spectroscopic techniques are increasingly being investigated to quantify these fractions and total organic carbon (TOC). This study examined the change in MIR-predicted pools of TOC, POC, HOC, and ROC in response to different crop management between two time periods (1981 and 2008) in a long-term wheat cropping trial in Queensland, Australia. The aims were (i) to assess the ability of MIR to detect changes in carbon stocks compared with direct measurements of TOC (LECO-TOC); and (ii) to assess how well the behaviour of POC, HOC, and ROC corresponded with the active, slow, and inert conceptual carbon pools. Significant declines in carbon stocks were observed over time using both LECO-TOC and MIR-predicted stocks of TOC, POC, HOC, and ROC, although MIR-TOC under-estimated loss by 27–30% compared with LECO-TOC. The decline in MIR-POC and MIR-HOC was consistent with the expected behaviour of the active and slow conceptual pools; however, the decline in ROC was not consistent with that of the inert pool. In addition, MIR measurements did not accurately detect differences in the rate of carbon loss under different crop management practices.