The potential use of amino acids by ruminal microorganisms converting them into microbial protein for ruminants makes it challenging to supplement these nutrients in an accessible form in animals’ diets. Several strategies to protect amino acids from ruminal degradation were reported, producing amino acids available for the protein used in the intestine called “bypass.” The intercalation of biomolecules in clay mineral minerals has gained notoriety due to its ability to support, protect, transport, physicochemical properties and non-toxicity. This study aimed to investigate the incorporation of L-lysine (Lys), L-methionine (Met), and L-tryptophan (Trp) amino acids in the clay minerals sepiolite (Sep) and Veegum® (Veg) using the adsorption method. The characterization techniques of X-ray diffraction and infrared spectroscopy indicated the presence of biomolecules in the inorganic matrices. Elemental and thermal analyzes monitored the percentages of incorporated amino acids. They showed better incorporation capacities for Veg, such as Met-Veg < Lys-Veg < Trp-Veg and Lys-Sep < Met-Sep < Trp-Sep for sepiolite, except for the incorporation of Met. Matrices provide a promising alternative for planning the administration of biomolecules, using essential amino acids as models, and may offer an alternative to improve functional diet strategies.