The prohibition of certain coccidiostats in poultry has created a need to seek an alternative to control Eimeria infection. The aim of this study was to evaluate the effects of effective microorganisms (EM) in a multi-strain probiotic (Bokashi®), with clinoptilolite as a feed supplement on the mRNA expression of tight junction proteins and redox enzymes in the caecal tissue of chickens infected with E. tenella. The integrity of the intestinal barrier was tested by determining the concentration of fluorescein isothiocyanate dextran (FITC-d) in the chicken’s serum. A total of 600 1-day-old Ross 308 male chickens received diets with a 0.5% or 0.8% concentration of the probiotic together with clinoptilolite. The experiment used 5 treatment groups, and a control group, each with 5 replicates with 20 birds. The results indicate that the use of the 8 kg/t of feed multi-strain probiotic together with clinoptilolite in the diet of poultry caused a significant reduction in the number of E. tenella oocysts in the faeces and caecum and significantly improved the growth rate of chicken broilers infected with E. tenella. In addition, the probiotic and clinoptilolite enhanced antioxidant processes in the caecal mucosa and reduced oxidative stress induced by E. tenella infection.