Mechanical forces and 3D topological environment can be used to control differentiation of mesenchymal stem cells (MSCs). However, the effects of physical and mechanical cues of the microenvironment on MSC fate determination have not yet been fully understood. This study investigates and compares the effect of mechanical stimulations on soft cellular microspheres when subjected to dynamic fluid compression. Microspheres were produced by gelation of bovine collagen type I with concentrations of 2 mg/ml and 1000–2000 hES-MP cells per 5 μl droplet. A loading condition of 10% dynamic loading was applied by a BOSE BioDynamic bioreactor for 15 and 40 min/day for 5 and 10 days on the cell-seeded collagen microspheres. Cell viability and proliferation, alkaline phosphatase activity and mineralization were compared with controls. Monitoring alkaline phosphatase level reported a significant increase in the enzyme activity by day 14 in loaded samples of 40 min/day loading protocol compared with other experimental conditions. Mineralization was assessed by measuring calcium, phosphorous concentrations and intensity of H&E and alizarin red S staining and showed the highest mineral accumulation in the loaded samples on day 28 post encapsulation. This study indicated that loading of very low cell number seeded on soft natural scaffold can encourage osteogenesis of cells by enhancing both early stage bone marker and mineralization. Self-assembled cell/collagen microspheres present exceptional cell delivery model in bone healing/repair process and field of regenerative medicine.