Fishing causes direct removal of individuals from wild populations but can also cause a physiological disturbance in fish that are released or discarded after capture. While sublethal physiological effects of fish capture have been well studied in commercial and recreational fisheries, this issue has been overlooked for the ornamental fish trade, where it is common to capture fish from the wild and discard non-target species. We examined metabolic responses to capture and discard procedures in the three-striped dwarf cichlid Apistogramma trifasciata, a popular Amazonian aquarium species that nonetheless may be discarded when not a target species. Individuals (n = 34) were tagged and exposed to each of four treatments designed to simulate procedures during the capture and discard process: 1) a non-handling control; 2) netting; 3) netting +30 seconds of air exposure; and 4) netting +60 seconds of air exposure. Metabolic rates were estimated using intermittent-flow respirometry, immediately following each treatment then throughout recovery overnight. Increasing amounts of netting and air exposure caused an acute increase in oxygen uptake and decrease in available aerobic scope. In general, recovery occurred quickly, with rapid decreases in oxygen uptake within the first 30 minutes post-handling. Notably, however, male fish exposed to netting +60 seconds of air exposure showed a delayed response whereby available aerobic scope was constrained <75% of maximum until ~4–6 hours post-stress. Larger fish showed a greater initial increase in oxygen uptake post-stress and slower rates of recovery. The results suggest that in the period following discard, this species may experience a reduced aerobic capacity for additional behavioural/physiological responses including feeding, territory defence and predator avoidance. These results are among the first to examine impacts of discard practises in the ornamental fishery and suggest ecophysiological research can provide valuable insight towards increasing sustainable practises in this global trade.