Global biodiversity loss is creating a more urgent need to understand the role organisms play in ecosystem functioning and mechanisms of control. Decomposition of dead organic matter is a key ecological process that ensures soil formation, nutrient availability, and carbon sequestration. To gain understanding of how biodiversity and ecosystems function together to control leaf‐litter decomposition processes in a tropical rain forest (Yasuní National Park, Ecuador), we predicted the consequences of the decomposition process using a protocol in which we systematically disassemble the structural functionality of the soil macrofauna communities. We (1) describe the structure and function of the edaphic communities in detail and (2) explore the functional consequences of structural changes in these communities using a non‐random exclusion experiment to simulate body size‐related extinctions. To do this, we manipulated access of five size classes of soil invertebrates to eight types of plant leaf‐litter resources. After measuring and identifying about 4400 soil individuals belonging to 541 morphospecies, 12 functional groups, and following the fate of about 2000 tree leaves in a 50‐ha plot, we showed that (1) soil invertebrate communities were composed of a few common and many rare morphospecies that included mostly leaf‐litter transformer groups, with the most morphospecies and the greatest abundance coming from Hymenoptera, Collembola, and Coleoptera; (2) our survey captured 63–74% of the total soil biodiversity of the study area (meaning there may be up to 860 morphospecies); (3) litter transformers covered the widest range of body volume, and all groups were evenly distributed at small and large spatial scales (i.e., we found no patterns of spatial aggregation); (4) changes in food web structure significantly altered biomass loss for only three of the eight leaf‐litter treatments, suggesting the decomposition process was highly resistant to drastic changes such as size‐biased biodiversity loss independent of resource quality. We conclude organic matter decomposition may depend on all non‐additive effects that arise from multi‐species interactions, including facilitation, interspecific interference competition, and top‐down control that predators exert over detritivores at all body size ranges.