Sodium sebacate salts have several industrial applications as additives, lubricants, and a metal self-healing promoter in general industry, and some derivatives also have wide applications in cosmetics and pharmaceutical fields. Calcium sebacate formation and precipitation can be detrimental for the systems where sodium sebacate is used. It is thus important to investigate their crystallization features. Sodium and calcium sebacate were prepared, purified, and crystallized with different approaches to carry out a full X-ray diffraction powder diffraction structural analysis since suitable single crystals cannot be obtained. The calcium sebacate crystal structure was solved by simulated annealing. Calcium ions form layers connected by straight “all trans” sebacate molecules, a conformation that is also suggested by Fourier-transform infrared spectroscopy FTIR data. Water molecules are caged within calcium layers. The crystal structure is characterized by the calcium layers bent by 10.65° with respect to the plane where sebacate chains lie, different from other dicarboxilic salts, such as cesium suberate, where the layers are perpendicular to the cation planes. The sodium sebacate crystal structure resulted in being impossible to be solved, despite several crystallization attempts and the different data collection approaches. FTIR spectroscopy indicates marked differences between the structures of calcium and sodium sebacate, suggesting a different type of metal coordination by carboxyls. Calcium sebacate shows a bis-bidentate chelating and bridging configuration ((κ2)−(κ1−κ1)−μ3−Carb), while for sodium sebacate, FTIR spectroscopy indicates an ionic interaction between sodium and the carboxyls. A thermogravimetric analysis TGA was carried out to assess the hydration states of the two salts. Calcium sebacate shows, as expected, a total weight loss of ca. 7%, corresponding to the single water molecule located in the crystal structure, while sodium sebacate shows no weight loss before total combustion, indicating that its structure is not hydrated. Scanning electron microscopy SEM images show different morphologies for calcium and sodium salts, probably a consequence of the different interactions at the molecular lever suggested by FTIR and TGA. The used approach can be extended to fatty acid salt in general, a still under-explored field because of the difficulty of growing suitable single crystals.