Anthocyanins are natural pigments responsible for color in fruits and flowers. They are unstable to diverse ambient conditions like pH, light, or the presence of ions. Thus, in industry, several techniques are employed to protect and use anthocyanins. Likewise, ancient Mayas used clay and indigo extract to prepare a pigment known as Maya Blue, resistant to time and chemicals. For this reason, this work aims to characterize the hibiscus extract and sepiolite bio-hybrids created according to Maya methodology and observe the stability of anthocyanins, which are color-responsible in flowers and fruits. Spectral analysis shows that anthocyanins and color were more stable than controls. Powder bio-hybrids show less color change under UV radiation and allochroic behavior in acid or alkaline atmospheres. At the same time, spectroscopy analyses and X-ray diffraction show no chemical interaction between sepiolite and hibiscus compounds. Our molecular dynamics with Reactive Force Fields (ReaxFF) studies reveal a similar behavior. Thus, our method protected the color of anthocyanins, in the temperature range from 15 to 35 °C. The interaction of hibiscus compounds with clay is due to van der Waals forces.