Culture of endothelial cells (ECs) embedded in 3D scaffolds of denatured collagen has shown tremendous therapeutic potential in clinical trials of tissue repair. It is postulated that these matrix-embedded ECs (MEECs) attain a differential phenotype similar to early progenitor forms, which cannot be attained in 2D culture. MEECs are compared to 2D-ECs and endothelial progenitor cells (EPCs) by secretome, phenotype, and genetic fingerprint, and are found to be altered from 2D-ECs on all levels, adopting an EPC-like phenotype. This manifests in elevation of CD34 expression—a progenitor cell marker—and protein secretion and gene expression pro-files that are similar to EPCs. Even more striking is that EPCs in 2D lose their phenotype, evident by the loss of CD34 expression, but are able to regain expression over time when embedded in the same 3D matrices, suggesting that future in vitro EPC work should use ME-EPCs to recapitulate in vivo phenotype. These findings elucidate the relationship between EPCs and the substratum-dependent regulation imparted by ECs which is critical to understand in order to optimize MEEC therapy and propel it into the clinic.