This study assessed the impact of Magni-Phi Ultra (MPU) inclusion on intestinal integrity and immunity in broiler chickens challenged with coccidia during peak and recovery phases. A total of 128 male Ross 708 broiler chicks were randomly allotted to one of four treatment groups (four chicks/cage). Treatments included an uninfected control (UUC); a coccidial challenge (CC) infected control (IUC); a CC fed salinomycin at 66 ppm (SAL); and a CC fed Magni-Phi Ultra at 0.11 g/kg of diet (MPU). At 16 days post-hatch, all birds in the CC groups were orally gavaged with a 3× dose of a live coccidia vaccine. At 5 dpi, the birds fed MPU and SAL showed decreased plasma FITC-d, oocyte shedding, and lesion scores and higher BWG compared to the IUC birds (p < 0.05). Jejunum IL-17, IL-10, and IFN-ϒ mRNA expression was higher in the IUC compared to the UUC (p < 0.05) group at 5 dpi. At 12 dpi, the birds fed MPU or SAL had lower plasma FITC-d and jejunum IFN-ϒ and IL-10 mRNA expression compared to the IUC birds (p < 0.05). This study indicates that MPU supports intestinal integrity and mucosal immune responses during the peak and recovery phases of infection, which may lead to improved health and performance.