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Procedures to obtain skin secretions in frogs may induce stress from handling or injection with stress-associated hormones (norepinephrine). We investigated the metabolic costs of procedures used to assess amphibian antimicrobial capacity and skin microbiome. We randomly assigned 48 adult coqui frogs (Eleutherodactylus coqui) to four treatments: microbiome depletion, antimicrobial peptide (AMP) depletion, microbiome and AMP depletion, and an unmanipulated control group. Microbiome depletion was achieved by soaking frogs in an antibiotic cocktail bath, whereas the AMP depletion was done by injection of norepinephrine followed by a buffer bath. We used a flow-through Sable Systems Field Metabolic System to collect respirometry data following a 30-minute acclimation period to respirometry chambers. Respirometry data were collected at three timepoints: (1) Baseline at 2-3 weeks prior to treatment; (2) Post-treatment representing 2 days after AMP depletion and 4 days after microbiome depletion; and (3) Final data at 6 weeks post-treatment. Then, to assess the effects of norepinephrine injection at a shorter timescale, a subset of 24 frogs that had not previously experienced AMP depletion were assigned to either AMP depletion or a buffer bath-only control group. Respirometry data collection began without acclimation to respirometry chambers, immediately after removing frogs from buffer baths. Over the 6-week period, we found no consistent treatment effects on metabolism in coqui frogs. At the shorter timescale, metabolism increased with time-since-handling and after norepinephrine injection. Our results show that standard procedures predicted to increase stress at the individual level do not have a lasting effect on whole-frog metabolism.