Tailoring diet to support a healthy gut microbiome is key for animal well-being. The gut metabolome, including all small molecules in the gut, is central to diet-microbiome-health interactions. While comprehension of the gut metabolome in companion animal nutrition is emerging, a substantial number of studies have been undertaken to elucidate the metabolomic shifts and identify specific marker metabolites influenced by diverse dietary interventions. By employing various metabolomic approaches, researchers have extensively documented the effects of different diet types, nutrient compositions, and dietary supplements on the gut metabolome in dogs and cats. Despite these advancements, there remains several notable limitations, including a lack of integrated microbiome analysis, incomplete understanding of specific marker metabolites, and an over-reliance on extrapolating findings from human studies. Therefore, this review aims to summarize the current understanding of the canine and feline gut metabolome, while exploring future possibilities and challenges for the field.