Horses reared for meat production are fed high amounts of cereal grains in comparison with horses raised for other purposes. Such feeding practice may lead to risk of poor welfare consequences. The aim of this study was to investigate the effects of two feeding practices on selected metabolic parameters and production aspects. Nineteen Bardigiano horses, 14.3 ± 0.7 months of age, were randomly assigned to two groups—one fed with high amounts of cereal grains (HCG; n = 9; 43% hay plus 57% cereal grain‐based pelleted feed) vs. one fed with high amounts of fibre (HFG; n = 10; 70% hay plus 30% pelleted fibrous feed)—for 129 days. At slaught on abattoir, biological and tissue samples were collected to evaluate the microbiological contamination of mesenteric lymph nodes and liver; selected meat quality traits (chemical composition and fatty acid profile of the Longissimus thoracis et lumborum muscle); and the oxidative status of the horse. A linear mixed model was used: dietary treatment and sex were fixed effects and their interaction analysed on production and metabolic parameters as dependent variables. Results showed an increased intestinal permeability in the horses fed HCG compared to HFG, according to the significant increased total mesophilic aerobic bacteria counts in mesenteric lymph nodes (p = 0.04) and liver samples (p = 0.05). Horses in HCG showed increased muscle pH (p = 0.02), lighter muscle colour (L) (p = 0.01), increased intramuscular fat concentrations (p = 0.03), increased muscle glutathione peroxidase and superoxide dismutase activities (p = 0.01 and p = 0.03, respectively). Moreover, horses in HCG had lower muscle water holding capacity at interaction with sex (p = 0.03, lower in female), lower muscle protein content (p = 0.01), lower concentration of muscle PUFAs (p = 0.05) and lower plasma catalase activities (p = 0.05). Our results showed that feeding a high cereal grains diet can have global effects on horse physiology, and thus represents a threat for their welfare.