Duchenne muscular dystrophy (DMD) is one of the most severe degenerative myopathies. In the early stages of the disease, muscle is exposed to continuous cycles of degeneration and regeneration; over time, regenerative potential is exhausted, and necrosis prevails leading to fat and fibrotic infiltration. As of today, the cellular and molecular determinants responsible for this functional exhaustion remain still to be fully characterized. Timely coordination of the different cellular components is paramount for the correct execution of repair program; loss, interference or perturbation of cellular crosstalk will invariably result in delayed or aberrant regeneration. To pinpoint the mechanisms underpinning repair impairment in DMD it is therefore necessary an approach that will not only consider the role of the specific components separately but also will be able to evaluate their potential synergy. To bridge this gap here we present a multi-omic approach to monitor simultaneously the events occurring in the stem cell and in the surrounding niche. Our strategy will help elucidate the determinants interfering with regeneration in DMD. Taking advantage of the integration of scRNAseq, scATACseq and Spatial Transcriptomics, we have profiled during disease progression the evolution of muscle-resident cellular populations to identify dysfunctional subfractions and deregulated crosstalk. Our dataset could serve as basis for future studies aimed at the identification of novel biomarkers and lay the foundation for new therapeutic approaches to promote muscle regeneration.