Extracellular matrix‐based bio‐scaffolds are useful for tissue engineering as they retain the unique structural, mechanical, and physiological microenvironment of the tissue thus facilitating cellular attachment and matrix activities. However, considering its potential, a comprehensive understanding of the protein profile remains elusive. Herein, we evaluate the impact of decellularization on the human amniotic membrane (hAM) based on its proteome profile, physicochemical features, as well as the attachment, viability, and proliferation of umbilical cord‐derived mesenchymal stem cells (hUC‐MSC). Proteome profiles of decellularized hAM (D‐hAM) were compared with hAM, and gene ontology (GO) enrichment analysis was performed. Proteomic data revealed that D‐hAM retained a total of 249 proteins, predominantly comprised of extracellular matrix proteins including collagens (collagen I, collagen IV, collagen VI, collagen VII, and collagen XII), proteoglycans (biglycan, decorin, lumican, mimecan, and versican), glycoproteins (dermatopontin, fibrinogen, fibrillin, laminin, and vitronectin), and growth factors including transforming growth factor beta (TGF‐β) and fibroblast growth factor (FGF) while eliminated most of the intracellular proteins. Scanning electron microscopy was used to analyze the epithelial and basal surfaces of D‐hAM. The D‐hAM displayed variability in fibril morphology and porosity as compared with hAM, showing loosely packed collagen fibers and prominent large pore areas on the basal side of D‐hAM. Both sides of D‐hAM supported the growth and proliferation of hUC‐MSC. Comparative investigations, however, demonstrated that the basal side of D‐hAM displayed higher hUC‐MSC proliferation than the epithelial side. These findings highlight the importance of understanding the micro‐environmental differences between the two sides of D‐hAM while optimizing cell‐based therapeutic applications.