A novel approach that preserved most mesenchymal stem cell (MSC) characteristics was developed using MSC encapsulation in a hydrogel based on hyaluronic acid (HA). An optimized HA-hydrogel composition, whose characteristics were assessed by scanning electron microscopy and viscoelastic property analyses, as well as the more favorable MSC seeding density, was established. These optimal three-dimensional MSC culture conditions allowed morphological cell remodeling, maintained the expression of stem cell markers over 28 days of culture, and preserved MSC differentiation plasticity. In addition, MSCs in HA-hydrogel submitted for 7 days to mechanical constraint that aimed at mimicking in vivo cardiac beat displayed enhanced cell survival by more than 40% compared to static culture conditions. Thus, the optimized HA-based hydrogel provides a niche for MSCs, which preserves their properties and opens ways for cell therapy, in particular in aortic repair medicine.