Cell-based therapy in regenerative medicine is a powerful tool that can be used both to restore various cells lost in a wide range of human disorders and in renewal processes. Stem cells show promise for universal use in clinical medicine, potentially enabling the regeneration of numerous organs and tissues in the human body. This is possible due to their self-renewal, mature cell differentiation, and factors release. To date, pluripotent stem cells seem to be the most promising. Recently, a novel stem cell niche, called multilineage-differentiating stress-enduring (Muse) cells, is emerging. These cells are of particular interest because they are pluripotent and are found in adult human mesenchymal tissues. Thanks to this, they can produce cells representative of all three germ layers. Furthermore, they can be easily harvested from fat and isolated from the mesenchymal stem cells. This makes them very promising, allowing autologous treatments and avoiding the problems of rejection typical of transplants. Muse cells have recently been employed, with encouraging results, in numerous preclinical studies performed to test their efficacy in the treatment of various pathologies. This review aimed to (1) highlight the specific potential of Muse cells and provide a better understanding of this niche and (2) originate the first organized review of already tested applications of Muse cells in regenerative medicine. The obtained results could be useful to extend the possible therapeutic applications of disease healing.