This research evaluated two methods of arginine encapsulation, melt emulsification and nanoprecipitation, using a lipid matrix of carnauba wax and commercial polymers (Eudragit®) as a protective material. The ratios of wax–arginine were 1:1, 2:1, 3:1, and 4:1, while those of Eudragit® RS:RL were 30:70 and 40:60 in proportions of 1:0.5 and 1:1 Eudragit®–arginine. The microcapsules were morphostructurally characterized by scanning electron microscopy, and a microelement analysis was performed via energy-dispersive X-ray spectroscopy and Fourier transform infrared spectroscopy. Additionally, in vitro digestibility was used to determine the protection efficiency. Both encapsulated systems presented regular (crystals) and spherical (microcapsules) polyhedral morphologies. Qualitative nitrogen decreased significantly as the wax ratio increased in the wax–arginine formulations. The formulations with a 1:1 Eudragit:–arginine ratio (1000 mg arginine) produced a higher nitrogen content in the encapsulated systems than the formulations containing 500 mg of arginine. The 2:1 and 3:1 wax–arginine formulations had the lowest degradability after 5 h of rumen fluid exposure (40.7 and 21.26%, respectively) in comparison with 100% unencapsulated arginine. The 3:1 wax–arginine formulation is an efficient encapsulating system which protects against rumen degradation. The more intense absorption bands at 1738 cm−1 and 1468 cm−1 associated with the C=O and C-H groups in carnauba wax indicate that arginine was more protected than in the other systems.