Companion animals such as dogs and cats play a crucial role in modern families. Their overall health is significantly influenced by their gut health, with many health disorders arising from disturbances in the gut microbiome. Our review highlights the ability of probiotics and nutraceuticals to modify the gut microbiota and enhance gastrointestinal health in canine and feline species. We investigated the effects of probiotics and natural antioxidant molecules on digestion, immunological response, and barrier integrity in gastrointestinal health studies concerning dogs and cats. The analysis indicated that probiotics influence gut microbiota composition in a positive manner, enhance digestion, augment the immune response, and help to maintain barrier integrity. Additionally, natural products with antioxidant molecules showed the potential to improve gut health and protect pets from various illnesses. We concluded by advocating the need for more studies in this direction to fully understand their effects and optimize their use in veterinary medicine.