Using density functional theory calculations motivated by aberration-corrected electron microscopy, we show how the atomic structure of a fully epitaxial Co2MnSi/Ag interfaces controls the local spin-polarization. The calculations show clear difference in spin-polarization at Fermi level between the two main types: bulk-like terminated Co/Ag and Mn-Si/Ag interfaces. Co/Ag interface spin-polarization switches sign from positive to negative, while in the case of Mn-Si/Ag, it is still positive but reduced. Cross-sectional atomic structure analysis of Co2MnSi/Ag interface, part of a spin-valve device, shows that the interface is determined by an additional layer of either Co or Mn. The presence of an additional Mn layer induces weak inverse spin-polarisation (-7%), while additional Co layer makes the interface region strongly inversely spin-polarized (-73%). In addition, we show that Ag diffusion from the spacer into the Co2MnSi electrode does not have a significant effect on the overall Co2MnSi /Ag performance.