Current technologies for measuring cancer metabolism have limited clinical utility, as they require invasive tissue sampling and lack analytical versatility. Here, we report a programmable nanotechnology platform that directly profiles extracellular vesicles (EVs) in patient biofluids to comprehensively capture metabolic alterations within the tumour milieu. This technology, termed atomically configured catalytic hybrids for profiling extracellular vesicle metabolites (ACTIVE), employs dual-matched biotic–abiotic nanohybrids based on defect-engineered transition-metal dichalcogenide peroxidase to catalytically quantify EV-associated metabolites. Each hybrid comprises a biomimetic peroxidase grown in situ on a metabolite-responsive biological oxidase. By spatially and energetically aligning their redox centres to enable direct electron transfer, these hybrids establish efficient tandem catalytic cascades that detect low-abundance metabolites in complex samples, achieving >30-times-higher catalytic efficiency than wild-type catalysts. In EV profiling applications, ACTIVE enables measurements in native biofluids (>103-fold improvement), captures a broad spectrum of metabolites (including their conversion dynamics) across EV subpopulations from diverse cellular systems and reflects dynamic changes in metabolic pathways during cellular reprogramming. In clinical specimens, using only 5 µl of native ascites fluid, ACTIVE reveals distinct metabolic reprogramming signatures within the tumour milieu, enabling stratification of patient prognosis.