Capillary shear stress can improve osteogenic differentiation in muscle-derived precursor cells (MDPCs). This has implications for large-scale bioprocessing of cell therapies where capillary transfer is needed. The recovery, viability, and osteogenic differentiation potential of two subsets of MDPCs, early-adherent pre-plate 1 (PP1) and late-adherent PP3 populations, have been examined: PP1 MDPCs produced a greater degree of osteogenic differentiation than PP3 MDPCs, quantified by Alizarin Red S staining intensity (P < 0.05). For both cell populations, capillary flow-induced significant increases in Alizarin Red S staining (P < 0.05). However, PP1 cells were more susceptible to capillary flow-induced damage than PP3 cells and this was dependent on duration of exposure. Overall, results indicate that different cell subsets, even from within a single tissue, can respond variably to capillary shear stress, necessitating its precise monitoring and control.