Interest in applications of natural dye applications has increased because of their antibacterial properties and the possibility of extracting them from nature and residues. Using nanoclays as hosts to reinforce natural dye properties has been successfully demonstrated. However, no one has attempted to optimize the polymer matrix and hybrid pigment properties at the same time to ensure the best final properties for bio-composite applications. Using a statistical design for experiments, we propose the best combination of modifiers with the best nanoclay as the host of three natural dyes: chlorophyll, β-carotene, and betanine. Using the L9 Taguchi designs, we learned both the influence of the nanoclay structure, and the addition moment of surfactant, mordant salt, and silane modifiers. FTIR, XRD, DTG, integration sphere spectrophotometer, and UV-aging tests were used to characterize the hybrid pigments and epoxy bioresin composites. The degradation temperatures of the three natural dyes rose and the reinforcement of the stability of three natural dyes to UV–Vis radiation exposure was demonstrated, which avoided the migration of these dyes from bioresin to wet ribbing. Optimal results were obtained with hydrotalcite clay (calcined or not) by using surfactant and mordant before the natural dye, and before or after silane.