Spontaneous CP violation, such as the Nelson-Barr (NB) mechanism, is an attractive scenario for addressing the strong CP problem while realizing the observed phase of the Cabibbo-Kobayashi-Maskawa (CKM) quark-mixing matrix. However, not only the CKM phase but also the baryon asymmetric Universe requires sources of CP violation. In this study, we show that a supersymmetric NB mechanism can naturally accommodate the Affleck-Dine (AD) baryogenesis within a CP-invariant Lagrangian. The model provides flat directions associated with new heavy quarks. Focusing on one of the directions, we find that the correct baryon asymmetry is obtained with a sufficiently low reheating temperature which does not cause the gravitino problem. Some parameter space is consistent with the gravitino dark matter. We assess radiative corrections to the strong CP phase induced by gaugemediated supersymmetry breaking and CP-violating heavy fields and show that the strong CP problem is solved in a viable parameter space where the visible sector supersymmetric particles must be lighter than O(100) TeV. Even in the case that they are heavier than the TeV scale, our model predicts the neutron electric dipole moment within the reach of the near future experiments. Our model addresses the electroweak naturalness problem, strong CP problem, baryon asymmetric Universe, and dark matter. Then, the model may give a new compelling paradigm of physics beyond the Standard Model.