The placenta is essential for successful pregnancy outcome. Placental imaging is however challenging due to maternal breathing motion and fetal movements, making motion correction important for subsequent analysis. This study introduces an iterative model-based registration technique which incorporates a joint placenta-specific signal model for diffusion and relaxation data into the motion correction process. We compared our method to a pre-existing method used for contrast-enhanced data making use of principal component analysis. Our results suggest that the proposed method significantly improves alignment of free-breathing placenta relaxation and DW-MRI data and evidence that the precision of markers of function obtained in placenta can be improved.