The cosmological evolution of standard model Yukawa couplings may have major implications for baryogenesis. In particular, as highlighted recently, the CKM matrix alone could be the source of CP-violation during electroweak baryogenesis provided that the Yukawa couplings were large and varied during the electroweak phase transition. We provide a natural realisation of this idea in the context of Randall-Sundrum models and show that the geometrical warped approach to the fermion mass hierarchy may naturally display the desired cosmological dynamics. The key ingredient is the coupling of the Goldberger-Wise scalar, responsible for the IR brane stabilisation, to the bulk fermions, which modi fies the fermionic profiles. This also helps alleviating the usually tight constraints from CP-violation in Randall-Sundrum scenarios. We study how the Yukawa couplings vary during the stabilisation of the Randall-Sundrum geometry and can thus induce large CP-violation during the electroweak phase transition. Using holography, we discuss the 4D interpretation of this dynamical interplay between flavour and electroweak symmetry breaking.