Intercropping is a sustainable, eco-friendly, and economically beneficial cropping system. Elephant foot yam (EFY), a multifarious long-duration vegetable, takes 60 days or more to spread its canopy. Hence, this research assessed the impact of intercropping short duration vegetables, viz., cluster bean, radish, Amaranthus, and fenugreek, in elephant foot yam for two seasons (2021 and 2021/22). It included the analysis of parameters such as carbon accumulation, soil chemical properties, nutrient, enzyme, and microbial activities. The findings revealed that for both the seasons there was a significant (p < 0.01) rise in all the parameters examined in the intercropping patterns. Cluster bean (legume) outperformed the other intercrops utilised. Overall, carbon accumulation was improved by 54.40% when cluster beans were intercropped in EFY. Cluster bean intercropping increased the microbial and enzyme activities in the soil rhizosphere and improved soil organic carbon, microbial biomass carbon, nitrogen, phosphorus, and potassium by 31, 42, 28, 37, and 11%, respectively, compared to the sole crop. A positive correlation was observed between the soil microbes and enzyme activity with the soil chemical properties. As a result, the research concludes that intercropping cluster bean in EFY promotes carbon accumulation, soil nutrients, enzymes, and microbial community, which, in turn, favour the productivity of the elephant foot yam.