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Understanding trophic linkages within the soil food web (SFW) is hampered by its opacity, diversity, and limited niche adaptation. We need to expand our insight between the feeding guilds of fauna and not just count biodiversity. The soil fauna drive nutrient cycling and play a pivotal, but little understood role within both the carbon (C) and nitrogen (N) cycles that may be ecosystem dependent. Here, we define the structure of the SFW in two habitats (grassland and woodland) on the same soil type and test the hypothesis that land management would alter the SFW in these habitats. To do this, we census the community structure and use stable isotope analysis to establish the pathway of C and N through each trophic level within the ecosystems. Stable isotope ratios of C and N from all invertebrates were used as a proxy for trophic niche, and community-wide metrics were obtained. Our empirically derived C/N ratios differed from those previously reported, diverging from model predictions of global C and N cycling, which was unexpected. An assessment of the relative response of the different functional groups to the change from agricultural grassland to woodland was performed. This showed that abundance of herbivores, microbivores, and micropredators were stimulated, while omnivores and macropredators were inhibited in the grassland. Differences between stable isotope ratios and community-wide metrics, highlighted habitats with similar taxa had different SFWs, using different basal resources, either driven by root or litter derived resources. Overall, we conclude that plant type can act as a top-down driver of community functioning and that differing land management can impact on the whole SFW.