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• Intercropped maize-forage systems promote C cycling in aggregates and SOM fractions. • N fertilization of intercropped systems reduce aggregation by reducing soil pH. • Carbon stabilization in mineral surfaces does not increase with nitrogen addition. • Larger aggregates under palisade grass is only partially linked with root morphology. Intercropping maize with forage grasses is an economical and environmentally sound practice that is increasingly being adopted to enhance resilience in tropical agriculture. Although intensifying integrated cropping systems can increase the sequestration of carbon (C) from plant residues, it also unleashes priming of old soil C enhancing C cycling, particularly under nitrogen (N) fertilization. However, the extent of these competing processes in intercropped maize–forage systems is poorly understood. This four-year study assessed whether new C inputs from maize ( Zea mays ) intercropped with ruzigrass ( Urochloa ruziziensis ), palisade grass ( Urochloa brizantha ), or Guinea grass ( Megathyrsus maximum ) in the presence or absence of N fertilization affect soil aggregation and C cycling in the soil and within macroaggregates (>0.250 mm) and microaggregates (<0.250 mm) down the soil profile. C cycling was assessed by measuring variations in the abundance of the natural isotope 13 C. N fertilization of the intercropped maize–forage systems reduced the proportion of aggregates > 2 mm and the mean weight diameter of aggregates by reducing soil pH. Under N fertilization, the geometric mean diameter of aggregates were 42 % larger under palisade than under Guinea grass. New C inputs from intercropping maize with forage grasses promoted C cycling in bulk soil, particulate organic matter (POM), mineral-associated organic matter (MAOM), and macro- and microaggregates, although these effects were restricted to topsoil. No N fertilization increased ruzigrass C input into MAOM with no clear link with 13 C enrichment, suggesting that N fertilization does not impair C stabilization in this pool. Aggregates >2 mm and >0.5 mm were key sinks of C and N up to a soil depth of 40 cm in this intercropped system. Our findings provide insights into the extension of C cycling across SOM pools and aggregates, and the role of N management in intercropping maize forage systems.