Rapid environmental change forces long-lived plants like trees to immigrate into zones still occupied by phylogenetically distantly related species. Does such phylogenetic isolation (PI) change the trees’ ecosystem functioning such as litter decomposition? We studied oaks (Quercus petraea) of low and high PI, reciprocally transplanting their litters to identify effect of aboveground litter quality and belowground decomposer biota. Across 8 and 14 months we quantified decomposition (mass loss, C-loss and N-loss), decomposer biota (Acari, Collembola, microbes) and ¹³C/¹²C ratio. Across 14 months, aboveground PI retarded decomposition (mass and C loss). Across 8 and 14 months, above- and belowground PI extensively altered relationships between decomposition and abundances/diversities of different soil biota, reduced microbial activity and ¹³C/¹²C ratios. Overall, coexistence of trees with distant relatives impedes and severely re-organizes C and N recycling. Such negative ecosystem feedback might prevent trees from tracking and conserving abiotic niches under environmental change.