Soil organic matter (SOM) in agricultural soils is generally lower in cultivated and intensively managed cropping soils than in pasture soils. Cultivation during the transition from pasture to crop leads to a loss of SOM, which may affect soil functionality and subsequent agricultural productivity. However, it is unclear how management practices influence SOM dynamics following this transition. We investigated the impact of initial soil fertility and application of lime and nutrients (nitrogen (N), phosphorus (P) and sulfur (S)) on changes in soil carbon (C) during the transition from a permanent pasture to a crop. The pasture was managed over 20 years with fertiliser to generate soils with initial high and low fertility (referred to as P2 and P0, respectively), based on soil C, N, P and S concentrations. Prior to sowing, pasture residue was incorporated with three treatments applied: control, lime, and lime + nutrient. Two successive crops of triticale (Triticale (× Triticosecale)) were then grown. The P0 and P2 soils were again cultivated in March 2018 with incorporation of the triticale stubble residue (9 Mg ha^–1) in each of the three soil treatments. After the two successive cereal crops, higher whole-soil C stocks were retained in the P2 than the P0 soils (difference of 2.1 Mg C ha^–1 compared with an initial difference in stocks of 2.4 Mg C ha^–1), with smaller loss of whole-soil C in P2 soils receiving the lime and lime + nutrient treatments than in the P2 control (average 10.3%, 10.0% and 20.2% loss of total C, respectively, relative to initial levels of soil C). Loss of C from the more active >0.4-mm fraction as a proportion of total C loss was higher in the first year with incorporation of legume-based pasture residue than in the second year with incorporation of C-rich, nutrient-poor crop residue (56% and 18% of the loss of C from the whole soil was from the >0.4-mm fraction in the first and second year, respectively). In P2 soil, loss of C was smaller in the more stable <0.4-mm fraction in the lime and lime + nutrient treatments than in the control (average loss of 9.6%, 11.2% and 17.6%, respectively). By contrast, in the low-fertility (P0) soil, loss of C was greater in the <0.4-mm fraction in the lime treatment than in the control (12.3% and 3.4% loss, respectively) unless supplementary nutrients were added at the time of cultivation (7.0% loss). Narrowing of nutrient ratios (C : N and C : S) in the P0 whole soil over time suggested that the loss of soil C was associated with increased microbial processing of C in the coarse-fraction soil. Taken together, the results demonstrate that loss of C from the pasture soils after cultivation was lower for soil with initially higher soil fertility when lime was applied, and that for soils with lower initial fertility, application of nutrients in addition to those for crop growth reduced C mineralisation induced by lime application.