Lutein is an important antioxidant that quenches free radicals. The stability of lutein and hence compatibility for food fortification is a big challenge to the food industry. Encapsulation can be designed to protect lutein from the adverse environment (air, heat, light, pH). In this study, we determined the impact of mixed biopolymer systems based on bovine and caprine caseins, yeast β-glucan, and maltodextrin as wall systems for microencapsulating lutein dispersed in emulsified lipid carriers by spray drying. The performance of these wall systems at oil/water interfaces is a key factor affecting the encapsulation of lutein. The highest encapsulation efficiency (97.7%) was achieved from the lutein microcapsules prepared with the mixed biopolymer system of caprine αs1-II casein, yeast β-glucan, and maltodextrin. Casein type and storage time affected the stability of lutein. The stability of lutein was the highest (64.57%) in lutein microcapsules prepared with the mixed biopolymer system of caprine αs1-II casein, yeast β-glucan, and maltodextrin, whereas lutein microcapsules prepared with the biopolymer system of bovine casein, yeast β-glucan, and maltodextrin had the lowest (56.01%). The stability of lutein in the lutein microcapsules dramatically decreased during storage time. The antioxidant activity of lutein in the lutein microcapsules was closely associated with the lutein concentration.