Organo-modified layered materials characterization poses challenges due to their complexity and how other aspects such as contamination, preparation methods and degree of intercalation influence the properties of these materials. Consequently, a deep understanding of their interlayer organization is of utmost importance to optimize their applications. These materials can in fact improve the stability of photoactive molecules through intercalation, avoiding the quenching of their emission at the solid state, to facilitate their use in sensors or other devices. Two synthetic methods for the preparation of saponites with a cationic surfactant (CTABr) and a neutral chromophore (Fluorene) were tested and the obtained products were initially characterized with several complementary techniques (XRPD, SEM, TGA, IR, UV-Vis, Fluorescence and Raman spectroscopy), but a clear understanding of the organization of the guest molecules in the material could not be obtained by these techniques alone. This information was obtained only by thermogravimetry coupled with gas chromatography and mass spectroscopy (TGA-GC-MS) which allowed identifying the species present in the sample and the kind of interaction with the host by distinguishing between intercalated and adsorbed on the surface.