From orthopedic to neurological disorders, stem cells are used as platforms to understand disease mechanisms and considered as novel and promising treatment options, especially when the valid therapeutic approaches are unavailable or ineffective. There are different stem cell types in the literature, however the spindle-shaped, colony forming and multilineage-differentiating cells, also known as mesenchymal stem cells (MSC) are very popular, as MSC can be isolated from different tissues with minimal ethical concerns and without tumor formations, which make them easily accessible and widely used in vitro and in vivo studies. In the literature, MSC have been shown to have therapeutic effects and orchestrate the healing process via their mobilization, migration, differentiation capacities, immunomodulation properties and/or secretion of bioactive factors. Nowadays, MSC derived extracellular matrices (ECM), which are part of the secreted/produced bioactive molecules from MSC; draw attention of researchers due to their key roles in cell biology. Several groups have isolated ECM from in vitro cultured MSC using different methods of decellularization techniques for tissue-engineering approaches. According to current knowledge, decellularized ECM (dECM) influence growth, adhesion, differentiation, migration, apoptosis, proliferation, and phenotype of cells, covering almost all cellular events. In this comprehensive review we focused on MSC and the isolation methods and effects of MSC derived dECM (MSC-dECM).