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Organoclays are hybrids derived from an ion exchange of hydrophilic clays with quaternary ammonium salts. The exchange makes the clay hydrophobic and enables it to swell in non-aqueous systems; because of this property, organoclays are widely used as rheological additives in paints, inks, cosmetics and as pollutant absorbing agents in soil remediation programs. We studied the manufacturing process of organic–clay hybrids using one natural (Na-montmorillonite) and several synthetic clays (Na-fluorophlogopites) as precursors: organoclays prepared from synthesized clays are characterized by higher purity and reproducibility as well as specifically designed features. We prepared the organoclays using both conventional–hydrothermal and microwave hydrothermal processes, in order to compare the results obtained with two different heating methods under the same reaction conditions. We found that there are no significant differences in terms of kinetics of intercalation with lower-charged clays, while microwaves can lead to better results in the treatment of higher-charged clays.