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Multipotent stromal cells are considered attractive sources for cell therapy and tissue engineering. Despite numerous experimental and clinical studies, broad application of stromal cell therapeutics is not yet emerging. A major challenge is the functional diversity of available cell sources. Here, we investigated the regenerative potential of clinically relevant human stromal cells from bone marrow (BMSCs), white adipose tissue, and umbilical cord compared to mature chondrocytes and skin fibroblasts in-vitro and in vivo. Although all stromal cell types can express transcription factors related to endochondral ossification, only BMSCs formed cartilage discs in vitro that fully regenerated critical-sized femoral defects after transplantation into mice. We identified cell type-specific epigenetic landscapes as the underlying molecular mechanism controlling transcriptional stromal differentiation networks. Binding sites of commonly expressed transcription factors in the enhancer and promoter regions of ossification-related genes, including Runt and bZIP families, were accessible only in BMSCs but not in extra-skeletal stromal cells. This suggests an epigenetically predetermined differentiation potential depending on cell origin that allows common transcription factors to trigger distinct organ-specific transcriptional programs, facilitating forward selection of regeneration-competent cell sources. Last, we demonstrate that viable human BMSCs initiated defect healing through the secretion of osteopontin and contributed to transient mineralized bone hard callus formation after transplantation into immunodeficient mice, which was eventually replaced by murine recipient bone during final tissue remodeling., Here we provided data and R script for the gene expression profiling meta-analysis of different stromal cells. Scripts for processing ATAC and CHIP-seq data are also provided. The epigenetic raw data is available at Gene Expression Omnibus (GEO), NCBI, https://www.ncbi.nlm.nih.gov/geo/, Accession-ID: GSE182497.