A 2 x 2 x 2 factorial arrangement of treatments was used to investigate the effects of two Iranian wheat cultivars (Alvand or Atrak), two processing methods (dry heating or microwave), and two enzyme (Kemzyme) levels on the performance, microbiota activity, and intestinal morphology of broiler chickens. A total of 320 broiler chickens were assigned to 8 treatments with 4 replicate pens of 10 broiler chickens per pen. The results showed that birds that received Alvand cultivar with microwave processing and enzyme supplementation had greater weight gain and feed conversion ratio (FCR) than those that received Atrak cultivar (P <.05). The total bacteria count in ileo-caecum was greater in broilers fed wheat-based diets with enzyme and dry heating process (P <.05). Atrak cultivar, microwave processing, and enzyme supplementation increased the population of Lactobacilli in broiler chickens (P <.05). Besides, the inclusion of enzyme decreased the population of E. coli in the ileo-caecum of broiler chickens (P <.05). The morphological traits of the intestine were greater in birds that received Atrak cultivar with enzyme supplementation and microwave treatment (P <.05). In conclusion, the positive effects of microwave processing and enzyme supplementation on the growth performance and intestinal morphology were clearly evident for broiler chickens.