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Simple Summary Chronic enteropathies are common gastrointestinal diseases in domestic dogs characterised by long-term duration, often impairing quality of life both for pets and owners. It has been demonstrated that the gut microbial community plays a central role in defining the host health status. Indeed, among a variety of biological functions, gut microbiota are involved in the metabolism of nutrients, in training the immune system and in preventing the gastrointestinal ecosystem from being colonised by pathogens. In chronic intestinal diseases, the equilibrium of the gut microbial population is largely impaired, as a consequence of both disease and therapy (e.g., antibiotic treatment). Faecal microbiota transplantation has the aim to restore a balanced microbial population in the patient by simply implanting a healthy gut microbiota derived from a healthy donor to a diseased animal. In doing so, the eubiotic community—and the extensive network of beneficial cross-feeding interactions—are transferred to the receiver’s gut as a whole, favouring the patient to renew a healthy intestinal ecosystem. In this work, we report the encouraging results of a faecal transplantation on a 9-year-old dog suffering from chronic enteropathy for the last 3 years. After the treatment, the dog’s appetite, body weight and vitality were restored, with complete disappearance of gastrointestinal and systemic symptoms. Abstract Chronic enteropathies (CE) are gastrointestinal diseases that afflict about one in five dogs in Europe. Conventional therapeutic approaches include dietary intervention, pharmacological treatment and probiotic supplements. The patient response can be highly variable and the interventions are often not resolutive. Moreover, the therapeutic strategy is usually planned (and gradually corrected) based on the patient’s response to empirical treatment, with few indirect gut health indicators useful to drive clinicians’ decisions. The ever-diminishing cost of high-throughput sequencing (HTS) allows clinicians to directly follow and characterise the evolution of the whole gut microbial community in order to highlight possible weaknesses. In this framework, faecal microbiome transplantation (FMT) is emerging as a feasible solution to CE, based on the implant of a balanced, eubiotic microbial community from a healthy donor to a dysbiotic patient. In this study, we report the promising results of FMT carried out in a 9-year-old dog suffering from CE for the last 3 years. The patient underwent a two-cycle oral treatment of FMT and the microbiota evolution was monitored by 16S rRNA gene sequencing both prior to FMT and after the two administrations. We evaluated the variation of microbial composition by calculating three different alpha diversity indices and compared the patient and donor data to a healthy control population of 94 dogs. After FMT, the patient’s microbiome and clinical parameters gradually shifted to values similar to those observed in healthy dogs. Symptoms disappeared during a follow-up period of six months after the second FMT. We believe that this study opens the door for potential applications of FMT in clinical veterinary practice and highlights the need to improve our knowledge on this relevant topic.