Nanocomposites based on polyamide 6 (PA6) and commercial layered silicates have been prepared by both in situ polymerization and melt compounding. The main aim of the present work has been centred on compatibilizer degradation, caused by the preparation conditions, in terms of nanocomposite end features. Two montmorillonite (MMT)-type, organically-modified clays (OMLS), namely Cloisite 30B ® and Nanofil 784 ®, and a sodium MMT (Cloisite Na ®) have been studied. Thermal properties of the layered silicates have been evaluated by TGA, IR, WAXD and pyrolysis–gas–mass. In order to better assess the influence of high temperature processes on clay modifications, a thermal treatment which mimics the conditions used during the in situ polymerization (4 h at 250 °C) has been applied on layered silicates. The above treatment, besides the elimination of absorbed water from all the clays, turned out to prove noteworthy differences in compatibilizer modification for the two organoclays. Indeed, in the case of Closite 30B ® only a removal of organic molecules outside the silicate galleries and a likely reorganization of those present inside the galleries have been detected, while a relevant chemical modification of Nanofil 784 ® compatibilizer has been conversely found. As far as nanocomposite characteristics are concerned, the latter have been found to depend on both the preparation method and clay type. In the case of in situ polymerization, also thermally-treated layered silicates, coded (T), have been used, in order to put more clearly in evidence the role of compatibilizer decomposition on nanocomposite formation and properties. Indeed, nanocomposite samples containing Closite 30B ®(T) have been found to be completely exfoliated, while the same thermal treatment seems to make worse the properties of those based on Nanofil 784 ®(T). Furthermore, with respect to nanocomposites based on pristine clays, samples containing thermally-treated silicates turned out to be different in terms of both molecular mass and crystal structure of the polymer matrix. Namely, PA6 γ-form seems to be promoted for all nanocomposites prepared in such a way, probably because of water removal at high temperature, which makes –OH groups of the layered silicate more free to interact with polyamide chains, thus causing a restriction of their mobility.