The present study investigated the effects of dietary supplementation with several Bacillus strains on growth performance, intestinal inflammatory and anti-inflammatory cytokines, anti-oxidants and tight junction (TJ) protein mRNA expression in broiler chickens challenged with mixed coccidia infection (oocysts of Eimeria tenella, Eimeria maxima and Eimeria acervulina). Ten different Bacillus strains were screened for their beneficial effects on coccidiosis challenge by measuring relative body weight gain (RBWG), lesion score, and total oocyst count. Three out of ten Bacillus strains were evaluated in depth by measuring RBWG, lesion score, total oocyst count, and the gene expression of proinflammatory (IL-6 and IL-8), anti-inflammatory (IL-10 and TGF-β), anti-oxidant (SOD1 and HMOX1), and TJ (JAM2 and occludin) proteins. Our results showed that out of the ten different Bacillus strains, chickens fed with three strains, one Bacillus licheniformis and two Bacillus amyloliquefaciens, showed significantly higher RBWG, lower lesion scores (ceca, jejunum, and duodenum), and lower total fecal oocyst counts compared to non-Bacillus-fed control chickens. Post-coccidia challenge, the RBWG for the Bacillus-fed groups were 95–100 % as opposed to the control birds (70 %) at 6 days post infection (dpi) and 10 dpi. Similarly, the lesion scores for three organs were around 0.8-0.9 for the Bacillus-fed groups as opposed to control birds (lesion score range ∼1.4–2). The total oocyst counts were much lower in the Bacillus-fed group (10–20 folds lesser) than the control group. Furthermore, the Bacillus-fed groups showed differential gene expression at 3 dpi in different tissues, such as caecum, jejunum, and duodenum. Bacillus-fed chickens showed significant pro- and anti-inflammatory responses and higher expression of anti-oxidants and TJ proteins in the ceca, duodenum, and jejunum. Overall, our results demonstrated that dietary supplementation with Bacillus strains as direct-fed microbials (DFM) significantly improved the body weight gain after mixed coccidia challenge compared to non-Bacillus-fed and coccidia challenged control group. In conclusion, the results of this study are promising and indicate the many beneficial effects of DFM-supplementation in poultry diets to reduce the negative consequences of enteric diseases and to decrease economic losses imposed by coccidia infection in chickens.