The conventional decaffeination processes consume a lot of energy and use many chemical solvents that can be harmful to both the environment and human health. Although there are four main methods of decaffeination, they all consume high amounts of energy and tend to degrade the taste of the decaffeinated coffee; some processes even use harmful chemicals such as methylene chloride. To address this problem, natural clay minerals are chosen as the adsorbents to extract caffeine from coffee beverages due to their unique micro and nano structures. Selective caffeine adsorption can be achieved by engineering the clay structures, including methods of interlayer spacing control, ion exchange, edge sites modification, secondary structure control, and structural polymerization. Three clay minerals have been tested, which are laponite, bentonite, and zeolite Y. For all three clay materials tested, they initially do not show any caffeine adsorption. However, with different engineering principles applied, different degrees of caffeine removal are achieved. The best result is 80% caffeine reduction after 2 minutes and 99.6% after 20 minutes in real coffee using 1 gram of clay per 100mL of coffee; this particular result was achieved through clay interlayer spacing control, secondary structure control, and structural polymerization of the bentonite clay. Moreover, with the HPLC analysis, the result showed that the material is fairly selective for the caffeine molecule, and during the decaffeinated coffee taste tests, most of the participants said that decaffeination with clay yield better taste coffee compared to conventional decaffeinated coffee. This new decaffeination process is much faster and versatile since it can reduce much of the caffeine in most of the beverages that contain caffeine in just a few minutes. Clay mineral structural engineering is a very promising technology for selectively removing caffeine molecules and has great potentials for the beverage industry.