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Alterations in neuronal and glial metabolism contribute to numerous neurodegenerative diseases, and the crosstalk between these two cell types (i.e., axoglial metabolic coupling) is at the center of extensive investigation. Metabolic alterations frequently culminate in mitochondrial dysfunction, but so far it has proven challenging to obtain cell-type-specific metabolic data from neuronal or glial mitochondria in mouse models of injury or disease. Magnetic immunocapture of genetically tagged mitochondria has emerged as a powerful strategy, yet existing methods are either incompatible with sensitive downstream multi omic workflows or not yet tested in complex tissues with highly heterogeneous cell populations. Here, I refined the “MITO-Tag” approach, which leverages a Cre dependent 3×HA EGFP OMP25 epitope tag localized to the outer mitochondrial membrane. Following enzymatic and mechanical dissociation, mitochondria were rapidly immunopurified from cortical neurons, oligodendrocyte lineage cells, and—accomplished here for the first time—peripheral nerve axons using anti-HA magnetic beads in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-compatible KPBS buffer. This method yields specific and structurally intact mitochondria, as confirmed by live-organelle imaging and Western blotting for compartment-specific markers (COXIV, VDAC, citrate synthase), with minimal contamination from other organelles. Proteomic analysis of brain-derived immunoprecipitates (IPs) revealed mitochondrial enrichment comparable to existing magnetic immunopurification workflows. By enabling multi-omic mitochondrial profiling from moderate-abundance cell types within complex tissues, this method provides a versatile tool for investigating mitochondrial involvement in neurological disease and injury in vivo. Notably, isolation from peripheral nerve axons now offers the ability to characterize Wallerian degeneration and axoglial metabolic coupling mechanisms at an unprecedented resolution.