Siliceous concretions (nodules), from two different geological settings—the Apulian platform margins in Kefalonia island, and the Ionian Basin in Ithaca, Atokos, and Kastos islands—have been studied both in the field and in the laboratory. Nodule cuttings are mainly characterized by the development of a core, around which a ring (rim) has been formed. Mineralogical study, using X-ray powder diffraction (XRPD) analysis, showed that the rim is usually richer in moganite than the core. Homogeneous concretions, without discernible inner core and outer ring, were observed generally in both settings. Mineralogical analysis of the selected siliceous concretions from Kefalonia island showed the presence mostly of quartz and moganite, while calcite either was absent or participated in a few samples in minor/trace abundances. Moganite was generally abundant in all the samples from Kefalonia island. Concretions from the Ionian Basin showed a variation in the quartz, moganite, and calcite contents. Mineralogical differences were recognized both between the different studied geodynamic settings and internally in the same setting, but with different stages of development. The above-mentioned differential diagenesis on nodules evolution could be related to the presence and/or abundance of stylolites, later fluid flows, restrictions from one area to another due to synchronous fault activity, and the composition of substances dissolved in fluids. Moreover, the development of concretions produced secondary fractures in the surrounding area of the nodule-bearing rocks.