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This study was conducted to examine the effects of a plant extract mixture, a microencapsulated product composed of eugenol and garlic tincture (PE), on intestinal health in broilers under necrotic enteritis (NE) challenge. A total of 960 d-old mixed-sex Cobb 500 chicks were randomly distributed to 48-floor pens housing 20 birds per pen. Six treatments were applied: UC, unchallenged control; CC, challenged control; PE, challenged group plus PE; AM, challenged group plus antimicrobial (AM); FAP, challenged group plus a full dose of AM with PE; HAP, challenged group plus a half dose of AM with PE in starter, grower and finisher phases. Birds in the challenged groups were inoculated with <i>Eimeria</i> spp. on d 9 and <i>Clostridium</i><i>perfringens</i> on d 14. On d 16, the CC group had increased serum fluorescein isothiocyanate dextran (FITC-d), reduced villus surface area, goblet cell number, upregulated <i>CLDN1</i>, <i>JAM2</i> genes and reduced microbial diversity compared to the UC group (<i>p</i> < 0.05). Birds fed PE had reduced FITC-d, increased goblet cell number and <i>Bifidobacterium</i> compared to the CC group (<i>p</i> < 0.05). Birds fed PE had reduced <i>CLDN5</i> expression in male birds, and <i>Bacteroides</i> spp. in female birds than CC group (<i>p</i> < 0.05). These findings suggest that PE supplementation mitigates the effect of NE by improving the intestinal health of birds.