The fungal disease chytridiomycosis (causative agent Batrachochytrium dendrobatidis [Bd]) is a primary contributor to amphibian species declines. The morphological and physiological reorganization that occurs during amphibian metamorphosis likely increases the vulnerability of metamorphs to Bd. To address this, we exposed pro-metamorphic tadpoles of Fleay's barred frog (Mixophyes fleayi) to Bd and sampled skin and liver sections from control and exposed animals throughout metamorphosis (Gosner stages 40, 42 and 45). We used an untargeted metabolomics approach to assess the metabolic impacts of Bd infection during the critical metamorphic stages, extracting metabolites from sampled tissues and analysing them via Nuclear Magnetic Resonance spectrometry. Most exposed animals became moribund at Gosner stage 45, while a subset seemingly cleared their infections. Metabolite abundance varied throughout development, with Gosner stage 45 samples distinct from previous stages. Clinically infected animals at Gosner stage 45 exhibited profound metabolic dysregulation (e.g., upregulation of amino acid biosynthesis and degradation) in comparison to uninfected groups (negative controls and 'cleared' animals). Despite showing parallels with previous metabolomic analyses of Bd-infected adult frogs, we identified variations in our results that could be attributed to the dramatic changes that characterise metamorphosis and may be driving the heightened vulnerability observed in metamorphic amphibians.