Mitochondrial dysfunction is prevalent in the aging gastrointestinal tract. We investigated whether mitochondrial function in aging colonic crypts and exercise influences microbial gut communities in mice. Twelve PolgA^mut/^mut mice were randomly divided into a sedentary and exercise group at 4 months. Seven-aged matched PolgA^+/+ mice remained sedentary throughout. Stool samples were collected at 4, 7, and 11 months, and bacterial profiling was achieved through 16S rRNA sequencing profiling. Mitochondrial enzyme activity was assessed in colonic epithelial crypts at 11 months for PolgA^mut/^mut and PolgA^+/+ mice. Sedentary and exercised PolgA^mut/^mut mice had significantly higher levels of mitochondrial dysfunction than PolgA^+/+ mice (78%, 77%, and 1% of crypts, respectively). Bacterial profiles of sedentary PolgA^mut/^mut mice were significantly different from the sedentary PolgA^+/+ mice, with increases in Lactobacillus and Mycoplasma, and decreases in Alistipes, Odoribacter, Anaeroplasma, Rikenella, Parabacteroides, and Allobaculum in the PolgA^mut/^mut mice. Exercise did not have any impact upon gut mitochondrial dysfunction; however, exercise did increase gut microbiota diversity and significantly increased bacterial genera Mucispirillum and Desulfovibrio. Mitochondrial dysfunction is associated with changes in the gut microbiota. Endurance exercise moderated some of these changes, establishing that environmental factors can influence gut microbiota, despite mitochondrial dysfunction.