Study of cell‐biomaterial interaction is a crucial aspect of bone tissue engineering to find a state‐of‐the‐art functional substitute. In present study, the Wharton's jelly mesenchymal stem cells (hWJ‐MSCs) behavior on three‐dimensional biomimetic nano‐hydroxyapatite/chitosan/gelatin (nHA/CS/Gel) scaffolds was investigated. The outcome was assessed by histological, biochemical and morphological tests. Results indicated that hWJ‐MSCs attached onto the scaffold surface through membrane filopodia, uniformly spread throughout the contacting surface. It only took 3 days for the seeded cells to appear deep inside the scaffold, reflecting proper hWJ‐MSCs adhesion and migration, evidenced by both scanning electron microscope and hematoxilin and eosin assessments. Additionally, the present fabricated nHA/CS/Gel scaffold proved to be non‐toxic as it supported cell proliferation measured by 3‐(4,5‐dimethylthiazoyl‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay. Moreover, 3‐week culture of hWJ‐MSCs on scaffolds, immersed in osteogenic medium, rendered the microenvironment in favor of hWJ‐MSCs differentiation into osteoblast cells and extracellular matrix secretion. Finally, osteoblasts were immunologically positive for various osteogenic markers including osteocalcin, osteopontin, osteonectin, and alkaline phosphatase. Present findings indicate that nHA/CS/Gel scaffold appropriately harbored hWJ‐MSCs, stimulating their growth, migration, proliferation, and differentiation. hWJ‐MSCs‐loaded nHA/CS/gel substitute may therefore be considered as a suitable platform for the rising demand in in vivo bone repair studies. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 1166–1175, 2019.