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Woody breast (WB) is a meat quality problem that has caused significant economic losses for the poultry industry. Ross × Ross 708 chicks were randomly assigned to a 3 (diet) × 2 (cocci challenge) × 2 (sex) factorial arrangement of treatments. The three diets included the control diet (corn-soybean meal basal diet), antibiotic diet (basal diet + 6.075 mg bacitracin /kg feed), and probiotic diet (basal diet + 2.2 × 108 CFU Bacillus subtilis PB6 /kg feed). Birds in the cocci challenge treatment group received 20 × the live cocci vaccine as an inoculum on d 14. Growth performance and WB score were measured to understand the effects of management factors (diet and coccidiosis) on broiler growth and WB development. Results indicated that dietary bacitracin and Eimeria spp. increased WB incidence, body weight, and growth rate. Bacillus subtilis increased WB incidence in male broilers without affecting body weight and growth rate. The association of the development of the internal organs and skeletal muscle with WB myopathy incidence in broilers were evaluated. The digestion organs (proventriculus and gizzard) and the skeletal muscles (drumsticks, thighs, and wings) developed at lower rates in birds with WB. In addition, the effects of the dietary and challenge interventions on the gut microbiota diversity and composition associated with WB in broilers were investigated. Results showed that cocci challenge altered gut microbiota composition and various biosynthetic pathways. Maintaining a healthy gut ecosystem is critical for the reduction of WB incidence in broilers. Gene expression related to oxidative stress, gut barrier function, and inflammation in jejunal mucus was investigated. Results showed that WB is related to decreased mucin expression (MUC6) in mucus, indicating a correlation between WB incidence and a lessening of the secretion of gel-forming mucin. In conclusion, dietary antibiotic and probiotic and challenge intervention strategies increased WB incidence, and microbiota composition and gut health gene expression differed in broilers exhibiting WB myopathy.