Ediacaran Cloudina and Namacalathus are among the earliest shell-forming organisms. The debated carbonate phase of their skeletons, high-magnesium calcite or aragonite, has been linked to seawater chemistry and pCO2, yet independent constraints on the original mineralogy are lacking. We present a new method to distinguish primary skeletal mineralogy using δ44/40Ca values and trace element compositions of the skeletons and associated cements. Ca isotopes are useful because they are relatively insensitive to diagenetic alteration during burial, and they vary with the primary mineralogical phase of carbonate. We applied this method to microdrilled carbonate and cements associated with both Namacalathus and Cloudina skeletons from the Ediacaran Omkyk Member of the Nama Group in southern Namibia. These data demonstrate that both organisms originally produced aragonitic skeletons, which later underwent diagenetic conversion to calcite. We suggest that calcium isotopes can be used to further constrain unknown skeletal mineralogies through time and to reassess the relationship between seawater chemistry and the mineralogy of biocalcifiers.