Taking the MSSM as an effective low-energy theory, with a cut-off scale of a few TeV, can make significant modifications to the predictions concerning the Higgs and stop sectors. We investigate the consequences of such a scenario for electroweak baryogenesis. We find that the window for MSSM baryogenesis is extended and, most important, can be made significantly more natural. Specifically, it is possible to have one stop lighter than the top and the other significantly lighter than TeV simultaneously with the Higgs mass above the LEP bound. In addition, various aspects concerning CP violation are affected. Most notably, it is possible to have dynamical phases in the bubble walls at tree level, providing CP violating sources for Standard Model fermions.

20 pages, 2 figures; v2: added references