Submersion in the anaesthetic MS-222 is a well-established and effective method used during the euthanasia of fish, but the consequences of treatment with this anaesthetic for mitochondrial respiration are yet to be established. This is important to evaluate, as an increasing amount of research is conducting high-resolution respirometry to measure respiration across multiple species of fish, including looking at thermal sensitivity and mitochondrial responses to the warmer temperatures faced with climate change. Analysis often occurs after euthanasia with MS-222 without knowledge of how MS-222 itself affects any measured parameters of mitochondrial respiration, leaving potential for a misinterpretation of results. Here, high-resolution respirometry was conducted to explore how MS-222 affects oxidative phosphorylation in the brain and skeletal muscle of the three-spined stickleback, Gasterosteus aculeatus, which is a model species in evolutionary ecology. In the brain, differences in respiration were observed between three-spined sticklebacks euthanised with MS-222 and those where no anaesthetic was implemented. No differences between treatments were observed in the skeletal muscle, although variation between individuals was high and oxygen flux was lower than in the brain. Overall, this study highlights the need for a consistent method of euthanasia when conducting high-resolution respirometry in fish, as MS-222 may alter measures of oxidative phosphorylation.