The global expansion of tree plantations is often claimed to have positive effects for mitigating global warming, preventing soil erosion, and reducing biodiversity loss. However, questions remain unanswered about the impacts of plantations on belowground diversity and soil properties. Here, we examine how forestry plantations of exotic trees affect critical soil functions and the composition of invertebrate assemblages, by comparing invertebrate diversity and soil physico-chemical properties between non-native Pinus radiata plantations, and nearby native forests in a region of extensive plantation activity in south-central Chile. We quantified differences in diversity, abundance, and community composition of soil invertebrates, as well as fundamental soil properties such as soil water content, water infiltration, nutrient status, and pH. We show that in this landscape mosaic of native forest and plantations, both soil invertebrate communities and physical soil properties differed significantly between systems, despite similar soil origins and topographies. We found a significant loss of soil carbon and a major reduction in taxonomic and functional diversity of soil invertebrates in pine plantation sites. Soil biotic and abiotic characteristics of plantations differed significantly from native forests in plantation-dominated south-central Chile, with profound consequences for ecosystem processes and resilience to future climate change.