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Summary: Most of the protocols to analyze metabolic features of cell populations from different tissues rely on in vitro cell culture conditions. Here, we present a flow-cytometry-based protocol for measuring the respiratory chain function in permeabilized mouse microglia ex vivo. We describe microglial cell isolation, followed by analyzing complex I and II using flow cytometry. This optimized protocol requires a low input of permeabilized cells and can be applied to other ex vivo isolated cells or cells derived from cell cultures.For complete details on the use and execution of this protocol, please refer to Erny et al. (2021).