Restrictions on antibiotic use encourage researchers to seek natural substitutes with the same effects without adverse end effects resulting from antibiotic use. Savory and black pepper have been challenged against <i>Salmonella enteritidis</i> (<i>S. enteritidis</i>) bacterium using the spray dryer method to evaluate growth performance, antioxidant status, immune response, and intestinal health parameters in broilers. In this study, thyme essential oil (50%), savory (25%), peppermint (12.5%), and black pepper seeds (12.5%) were mixed to form essential oil-loaded spherical microcapsules with the particle size of 323 nm and encapsulation efficiency of 96.2%. The main bioactive compounds used in the core of microcapsules included thymol, carvacrol, p-cymene, γ-terpinene, and menthol. Moreover, modified starch (25%) and maltodextrin (55%) were used for the preparation of spherical microcapsules for the enclosed wall with 20% whey protein concentrate. The dietary addition of microcapsules containing essential oil significantly reduced the <i>S. enteritidis</i> population in both ileum and cecum (<i>P</i><0.05). The results revealed that the dietary inclusion of essential oil-loaded microcapsules significantly (<i>P</i><0.05) increased the villus height, villus width, V: C ratio, and the number of goblet cells and decreased the crypt depth. Microcapsules have antioxidant and antibacterial activity and their dietary use as feed additive at 0.5, 1, and 2 kg/t concentrations in broilers has been challenged and showed that the final weight, total feed intake, and FCR improved the body's antioxidant status, structure, and inflammation in the ileum tissue.