Preserving and enhancing soil organic carbon (SOC) stocks is one of the major objectives for sustainable agriculture. The exogenous nutrient supply along with returning crop residues, i.e., integrated residue-nutrient management, may increase carbon (C) cycling and residue-derived microbial biomass, and therefore to affect SOC stocks. However, there is a lack of knowledge about how the integrated residue-nutrient management, that balances the resource nutrient stoichiometry, facilitates the fate (or partitioning) of residue-C in physically defined SOC fractions. Hence, through a laboratory study, we quantified the fate of wheat residue (δ13C-enriched, 494‰) into sequentially separated physical SOC fractions, under the interaction of different residue rates (6.7 and 20.0 g kg−1 soil) and nutrient inputs (nil, low and high supplies of nitrogen, phosphorus, and sulfur) in two contrasting soils (Luvisol and Vertisol). The results showed that after 245 days, 42.7–54.2% of the newly-added residue-13C remained in organic matter (OM) fractions in the soils, with 22.1–40.8% in the light fraction [LF; defined as free particulate organic matter (f-POM)] and 13.9–19.5% in the heavy fraction [HF; defined as aggregate- & mineral-protected OM, which included silt-clay OM and occluded POM (o-POM)]. Following the sequential separation of HF, 8.3–15.3% of residue-13C was distributed to silt-clay OM and 4.2–6.1% to o-POM after 245 days. The high-residue rate (cf. low-residue) increased the amount of residue-C in SOC fractions. Narrowing the C-nutrient stoichiometric ratio in the residue treated soils via the exogenous nutrient input affected the proportional distribution of residue-C in SOC fractions at the high-residue rate only. With the high-residue rate in both soils, nutrient input (cf. no-nutrient) at both rates increased “new” residue-derived stable C formation in the HF by 17% or silt-clay associated OM by 27%, while decreased the distribution of residue-13C in the f-POM (LF) by 26% or o-POM by 18%. In the current study, soil type also affected the incorporation of residue-C in the organo-mineral fractions, i.e., 20% higher residue-C was incorporated in the silt-clay OM in the Vertisol than Luvisol. This study improved our knowledge on the distribution of residue-C in SOC fractions in response to integrated residue-nutrient management, which could be used to refine conceptual and mechanistic models for predicting changes in SOC storage.