Functional interactions between muscle (satellite) stem cells—MuSCs—and other cellular components of their niche (the fibro-adipogenic progenitors—FAPs) coordinate regeneration of injured as well as diseased skeletal muscles. These interactions are largely mediated by secretory networks, whose integrity is critical to determine whether repair occurs by compensatory regeneration leading to formation of new contractile fibers, or by maladaptive formation of fibrotic scars and fat infiltration. Here we provide the description of methods for isolation of FAPs and MuSCs from muscles of wild type and dystrophic mice, and protocols of cocultures as well as MuSC’s exposure to FAP- derived exosomes. These methods and protocols can be exploited in murine models of acute muscle injury to investigate salient features of physiological repair, and in models of muscular diseases to identify dysregulated networks that compromise functional interactions between cellular components of the regeneration environment during disease progression. We predict that exporting these procedures to patient-derived muscle samples will contribute to advance our understanding of human skeletal myogenesis and related disorders.