Layered double hydroxides (LDHs) are versatile materials used for intercalating bioactive molecules in the fields of pharmaceuticals, nutraceuticals and cosmetics, with the purpose of protecting them from degradation, enhancing their water solubility to increase bioavailability and improving their pharmacokinetic properties and formulation stability. Moreover, LDHs are used in various technological applications to improve stability and processability. The crystal chemistry of hydrotalcite-like compounds was investigated by X-ray powder diffraction (XRPD), automated electron diffraction tomography (ADT) and thermogravimetric analysis (TGA)-GC-MS to shed light on the mechanisms involved in ion exchange and absorption of contaminants, mainly carbonate anions. For the first time, ADT allowed a structural model of LDH_NO3 to be obtained from experiment, shedding light on the conformation of nitrate inside LDH and on the loss of crystallinity due to the layer morphology. The ADT analysis of a hybrid LDH sample (LDH_EUS) clearly revealed an increase in defectivity in this material. XRPD demonstrated that the presence of carbonate can influence the intercalation of organic molecules into LDH, since CO3 -contaminated samples tend to adopt d spacings that are approximate multiples of the d spacing of LDH_CO3 . TGA-GC-MS allowed intercalated and surface- adsorbed organic molecules to be distinguished and quantified, the presence and amount of carbonate to be confirmed, especially at low concentrations (<2 wt %), and the different types and strengths of adsorption to be classified with respect to the temperature of elimination.