Aragonite (along with calcite) is one of the most common polymorphs of the crystalline calcium carbonate that forms the skeletal structures of organisms, but it has relatively low preservation potential. Under ambient conditions and in the presence of water, aragonite transforms into calcite, the stable polymorph. Aragonite is also more soluble therefore, in water-permeable siliceous limestones (opokas) that are typical of Upper Cretaceous deposits of Poland and Ukraine, the primary aragonitic skeletons are either entirely dissolved and found as moulds and casts or transformed into secondary calcite, whereas the primary calcitic shells remain well preserved. Contrary to the common notion of the lack of aragonite in such porous carbonate deposits, we show that relics of aragonite can be preserved as a nacreous lining on cephalopod moulds or as thin, lenticular structures entrapped in neomorphic calcite. Based on the observed intermediate steps of aragonite alteration, we propose an extended model of nacre diagenesis. Among the originally aragonitic biota, only nautilids and ammonites have retained relics of pristine skeletons. Such selective preservation of only some aragonitic structures (nacre but not the prismatic aragonitic layers) points to the role of microstructural and biochemical differences between cephalopod shell layers that may set a threshold for the dissolution, dissolution/precipitation or preservation of original biomineral structures.