The isolation and molecular characterization of distinct cell populations from heterogeneous tissues are essential for investigating cell-type-specific functions and regulatory mechanisms, particularly within complex organs such as the skin. Here, we present a comprehensive workflow for isolating hair matrix cells from postnatal mouse skin using fluorescence-activated cell sorting (FACS) for gene expression and high-resolution chromatin profiling. The protocol begins with enzymatic dissociation of the skin to obtain a single-cell suspension, followed by immunolabeling with cell surface markers to enable precise FACS-based enrichment of the desired cell populations. A low-input CUT&Tag assay is then used to map histone posttranslational modifications, transcription factor binding sites, and DNA modifications. Importantly, this cell isolation strategy is compatible with a range of integrative multi-omics approaches including RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), whole-genome bisulfite sequencing (WGBS), and high-throughput chromosome conformation capture (Hi-C) using input material as low as ~100,000 cells per assay. Together, this methodology allows comprehensive, cell-type resolved analysis of the transcriptional and epigenetic landscapes in hair matrix keratinocytes in postnatal skin.