Nanocomposites based on biodegradable poly(ε-caprolactone) (PCL) and layered silicates (montmorillonite) modified by various alkylammonium cations were prepared by melt intercalation. Depending on whether the ammonium cations contain non-functional alkyl chains or chains terminated by carboxylic acid or hydroxyl functions, microcomposites or nanocomposites were recovered as shown by X-ray diffraction and transmission electron microscopy. Mechanical and thermal properties were examined by tensile testing and thermogravimetric analysis. The layered silicate PCL nanocomposites exhibited some improvement of the mechanical properties (higher Young's modulus) and increased thermal stability as well as enhanced flame retardant characteristics as result of a charring effect. This communication aims at reporting that the formation of PCL-based nanocomposites strictly depends on the nature of the ammonium cation and its functionality, but also on the selected synthetic route, i.e. melt intercalation vs. in situ intercalative polymerization. Typically, protonated ω-aminododecanoic acid exchanged montmorillonite allowed to intercalate ε−caprolactone monomer and yielded nanocomposites upon in situ polymerization, whereas they exclusively formed microcomposites when blended with preformed PCL chains. In other words, it is shown that the formation of polymer layered silicate nanocomposites is not straightforward and cannot be predicted since it strongly depends on parameters such as ammonium cation type and functionality together with the production procedure, i.e., melt intercalation, solvent evaporation or in situ polymerization.