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Integrated farming system (IFS) aims to diversify the agricultural landscapes by incorporating different components to meet the multifarious needs of the burgeoning population. The present study was undertaken to understand the impact of different cropping systems on soil organic carbon (SOC) stock, aggregate distribution, and aggregate associated organic carbon (AAOC) in 2-IFS models of varying sizes (0.4 and 0.8 ha) established during 2008–2009. After 10 years of the study, the fodder system registered the greatest TOC and carbon stocks across IFS models, with surface soil (0–15 cm) accumulating 17 and 13% higher TOC and C stock, respectively, in 0.4 and 0.8 ha models. In 0–15 cm, macroaggregates (Ma) represented the highest proportion (75–76%) in both models. Among cropping systems, the fodder system recorded the highest large macroaggregates in both IFS models. Within 0–30 cm depth, small macroaggregates are mostly found in the perennial system (fodder, guava+turmeric, and lemon intercropping system), indicating the potential to improve the aggregate stability over the seasonal (shorter duration) system. In general, micro aggregate (Mi) fraction was pre-dominant in sub-surface soil (17.35%). The maximum AAOC was found in Ma compared to Mi fractions, with approximately 67 and 63% of total carbon associated with Ma in 0.4 and 0.8 ha IFS models, respectively. Interestingly, the 0.8 ha IFS model had higher TOC (~11%) and carbon stock (~12%) than the 0.4 ha model, but AAOC did not show a similar result, indicating the influence of cropping systems on AAOC. The study indicated that the fodder-based production system had better performance in terms of soil physical health and increased aggregate stability and content of soil carbon. This is indicative of the advantages of perennial-based systems over seasonal- or annual-based cropping systems for soil sustainability in Eastern Indo-Gangetic Plains.