We show that the CKM matrix can be the source of CP violation for electroweak baryogenesis if Yukawa couplings vary at the same time as the Higgs acquires its vacuum expectation value. This offers new avenues for explaining the baryon asymmetry of the universe. These ideas apply if the mechanism explaining the flavour structure of the Standard Model is connected to electroweak symmetry breaking. We compute the resulting baryon asymmetry for various low-scale flavour models and different configurations of the Yukawa coupling variation across the bubble wall, and show that it can naturally be of the right order.