Tannins are compounds present in forage plants that, in small quantities in the diet of ruminants, produce protein complexes that promote passage through the rumen and use in the intestine. This study tested the hypothesis that beeswax (BW) and carnauba wax (CW) lipid matrices are effective encapsulants for creating bypass lysine (Lys) for ruminants, with tannin extracted from the Mimosa tenuiflora hay source enhancing material protection. Microencapsulated systems were made using the fusion–emulsification technique with a 2:1 shell-to-core ratio and four tannin levels (0%, 1%, 2%; 3%). The following eight treatments were tested: BWLys0%, BWLys1%, BWLys2%, BWLys3%, CWLys0%, CWLys1%, CWLys2%, and CWLys3%. Tannin inclusion improved microencapsulation yield and efficiency. CWLys3% had the highest microencapsulation efficiency and retained Lys. Lysine in BW and CW matrices showed higher thermal stability than in its free form. Material retention was greater in BW than CW. Rumen pH and temperature remained unaffected, indicating that BW and CW as the shell and tannin as the adjuvant are efficient encapsulants for Lys bypass production. The formulation CWLys3% is recommended as it is more efficient in protecting the lysin amino acid from rumen degradation.