Despite a myriad of studies confirming the interaction between biology and mechanics, the exact nature of the main mechanical stimuli and their influence on the bone regeneration processes are still unclear. The hypothesis of this study was that the outcome of peri-implant healing under different implant loading regimens can be explained by the influence of fluid flow on the combination of angiogenesis and osteogenesis through its influence on cell proliferation and differentiation. To investigate this hypothesis a mathematical model of bone regeneration was applied to simulate the peri-implant healing in an in vivo repeated sampling bone chamber for different axial micromechanical implant loading regimes. When mechanical loading was modeled to influence both osteogenic and angiogenic processes, a good agreement was observed between simulations and experiments concerning the amount of bone in the bone chamber, its radial and longitudinal distribution, and the bone-implant contact for different implant displacement magnitudes.