Agricultural soils play an important role in the global carbon (C) cycling and can act as a significant C sink if managed properly. The long-term (33 years) effects of no till (NT) v. conventional till (CT), stubble retention (SR) v. stubble burning (SB), and N fertiliser application (NF) v. nil N fertilisation (N0) on soil organic C sequestration, and their seasonal variations during the fallow period, were studied in a winter cereal–summer fallow cropping system under semi-arid subtropical climate in Queensland, Australia. The function of different density fractions of soil organic C in determining total organic C (TOC) dynamics and sequestration was investigated. Significant effect of NT, SR, or NF on soil organic C level was observed only in the top 10 cm soil and when they were practiced together, with the TOC contents being 1.1 to 3.4 t/ha higher under NT + NF + SR than under other treatments. There were significant seasonal fluctuations in TOC contents at different stages of the fallow period, and the lowest levels of TOC and treatment effects were observed in the late fallow period. Density fractionation of soil organic C showed that light fraction C (<1.6 g/cm³) declined rapidly during the fallow period and did not accumulate substantially in soil. TOC dynamics, either as a consequence of seasonal variations or as a long-term response to different farming practices, were predominantly controlled by the changes in the heavy fraction C (>1.6 g/cm³).