Vegetable production systems rely on frequent tillage to prepare beds and manage weeds, thereby accelerating losses of soil organic carbon (SOC). They are also characterised by scant crop residue input. Residue incorporation and organic fertiliser application could counteract SOC loss due to tillage. We tested this hypothesis in a Chromosol and a Vertosol in northern NSW, Australia, where the effects of incorporating sweet corn ('Zea mays' L. var. 'rugosa') residue in soil in a corn-cabbage ('Brassica oleracea' L.) rotation under either organic or conventional system on soil C fractions were studied during two rotation cycles (2 years). A laboratory experiment was conducted to isolate the effect of tillage on the soil organic matter (SOM) fractions, because both the residue-incorporated and without-residue treatments for organic systems received tillage for weed control in the field, whereas conventional systems did not. Residue incorporation increased particulate OC (POC) by 32% in the field experiment and 48% in the laboratory experiment, whereas dissolved OC was increased only in the organic system. Concentrations of mineral-associated OC (MOC) and total OC (TOC) were increased by residue incorporation in both field and laboratory experiments. Simulated tillage had a limited effect on POC, MOC and TOC, suggesting that cultivation for weed control may have only a minor effect on short-term SOM mineralisation rates. In both experiments, MOC accounted for ≤83% in the Vertosol and ≤73% in the Chromosol. Due to frequent tillage in vegetable production systems, physicochemical stabilisation of C predominates over protection through aggregation.