This research investigates the influence of synthesis kinetics on the structural and photocatalytic properties of chitosan–clay nanocomposites (Cs/MMT) and chitosan–hectorite nanocomposites (Cs/HET), employing an optimized initial stoichiometry of 1:3. Utilizing a variety of analytical techniques, including X-ray diffraction (XRD), transmission electron microscopy (TEM), and Fourier-transform infrared spectroscopy (FTIR), the study explores the structural evolution of the nanocomposites and their photocatalytic performance using semiconductor catalysts TiO2 and ZnO. The findings emphasize the significant impact of reaction kinetics, particularly after 3 h of reaction time, on the structural features of the nanocomposites. Notably, Cs/MMT demonstrates greater crystalline stability compared to Cs/HET due to variations in octahedral cavity occupancy in the initial clays. FTIR and TEM analyses depict the progressive evolution of the nanocomposites during the reaction, shedding light on how reaction kinetics drive the formation of specific bonds within the nanocomposites. In terms of photocatalytic activity, this study provides insights into the complex dynamics of photocatalytic degradation, with a specific focus on the performance of TiO2 and ZnO under diverse experimental conditions. The superior efficacy of TiO2 as a catalyst, particularly when integrated with Cs/MMT nanocomposites, is unequivocally demonstrated, with degradation rates exceeding 80%. This preference stems from TiO2 consistently exhibiting higher degradation rates compared to ZnO, attributed to structural disparities between montmorillonite and hectorite, influencing catalyst–support interactions. The findings underscore the critical importance of selecting suitable catalyst and support matrix combinations for optimizing performance in specific applications.