The objective was to determine the impact of feeding MCE on ruminal and intestinal morphology and microbiota composition of calves. A total of 10 male and 10 female crossbred (dairy × beef) calves (6 d of age) were assigned randomly to control (CTL; n = 10) or MCE-supplemented (TRT; n = 10) groups. The MCE was fed in the milk replacer and top-dressed on the calf starter during pre-weaning (6 to 49 d) and post-weaning (50 to 95 d) periods, respectively. Calves were slaughtered at 95 d to collect rumen and intestinal samples to determine volatile fatty acid (VFA) profile, mucosal morphology, and microbiota composition. The effects of MCE were analyzed by accounting for the sex and breed effects. Feeding MCE increased rumen papillae length (p = 0.010) and intestinal villus height: crypt depth (p < 0.030) compared to CTL but did not affect rumen VFA profile. The TRT had a negligible impact on microbial community composition in both the rumen and the jejunum. In conclusion, feeding MCE from birth through weaning can improve ruminal and small intestinal mucosa development of calves despite the negligible microbiota composition changes observed post-weaning.