Probiotics are being developed as alternatives to antibiotic growth promoters. The aim of the study was to investigate the effects of 2 novel strains of Bacillus pumilus and Bacillus subtilis on production, intestinal microbiota, gut health, and immunity of broilers raised under suboptimal conditions. Day-old chicks (Cobb 500, n = 2,073) were randomly assigned into 6 groups: Con group (group fed with basal diet), Ab group (group treated with virginiamycin), groups treated with 2 levels of B. pumilus (low dose: 3 × 108 cfu/kg of feed [BPL] and high dose: 1 × 109 cfu/kg [BPH]), and groups treated with 2 levels of B. subtilis (low dose: 3 × 108 cfu/kg [BSL] and high dose: 1 × 109 cfu/kg [BSH]). Production parameters were recorded weekly. Cecal tonsils and content as well as ileum samples were collected on day 14 and day 42. Cecal tonsils were used to sort T-regulatory cells (CD4+CD8–CD25+ and CD4+CD8+CD25+) to study expression of IL-10 and interferon gamma, whereas cecal content was used for bacterial culture. Ileum samples were used to measure gene expression of tight junction proteins, mucin, and cytokines. BW and feed intake increased in the Ab, BPL, BSL, and BSH groups compared with the Con group between day 35 and day 42. The CD4+CD8-CD25+ cells expressed high levels of IL-10 in the BSH group on day 14 and in the BPL, BSL, and BSH groups on day 42 and high levels of interferon gamma in the BPL, BSL, and BSH groups on day 14 and in the BSL and BSH groups on day 42. The expression of IL-10 and interferon gamma in CD4+CD8+CD25+ cells was higher only in the BSH group on day 14 and day 42. Cecal bacterial populations of genera, Lactobacillus (day 14 and day 42) and Clostridium (day 14), were higher in the BSH group. Expression of tight junction protein increased significantly in the ileum on day 14 in the BPL (occludin, zona occludens 1 [ZO-1]), BSL (occludin, ZO-1), and BSH (occludin, ZO-1, junctional adhesion molecule 2 [JAM-2]) groups compared with that in the Con group and declined in all groups except in the BSH group (occludin, ZO-1, JAM-2) on day 42. Expression of MUC2 and IL-17F increased in all groups on day 14 and remained high on day 42 in the BSL and BSH groups. Taken together, both Bacillus probiotics altered the intestinal and immune activities, particularly on day 14, suggesting beneficial influence of probiotics.