Coprophagy is a common behavior in domestic dogs, yet its effects on the intestinal microbiota and asymptomatic carriage of enteropathogens remain unclear. This study aimed to determine whether healthy coprophagic dogs differ from non-coprophagic dogs in fecal microbiota composition or prevalence of asymptomatic enteropathogen carriage. Forty-four clinically healthy dogs were prospectively enrolled, including 23 coprophagic and 21 non-coprophagic animals as reported by their owners. Ages spanned from 6 to 119 months old, including 19 mixed-breed dogs and 25 purebred dogs, and diet was not controlled for. Fecal samples were analyzed using quantitative PCR to determine the canine dysbiosis index, quantify core bacterial taxa, and detect selected enteropathogens, including Clostridium perfringens, Clostridioides difficile, Campylobacter jejuni, Salmonella spp., canine parvovirus, and toxin-associated genes. Demographic and microbiological data were compared between groups, with correction for multiple testing. No significant differences were observed between coprophagic and non-coprophagic dogs in dysbiosis index (q = 1), abundance of the core bacterial taxa evaluated (q = 0.17–1), or detection of enteropathogens (q = 0.734–1) after adjustment for multiple comparisons. Enteropathogens were absent or detected infrequently in both groups. These findings indicate that coprophagy in otherwise healthy dogs is not associated with measurable alterations in dysbiosis index, core fecal microbiota, or increased enteropathogen carriage.