Recent advancements have significantly enhanced our understanding of the crucial role animal microbiomes play in veterinary medicine. Their importance in the complex intestinal environment spans immune modulation, metabolic homeostasis, and the pathogenesis of chronic diseases. Dysbiosis, a microbial imbalance, can lead to a range of diseases affecting both individual organs and the entire organism. Microbial disruption triggers inflammatory responses in the intestinal mucosa and disturbs immune homeostasis, increasing susceptibility to toxins and their metabolites. These dynamics contribute to the development of intestinal lymphoma, necessitating rigorous investigation into the role of microbiota in tumorigenesis. The principles explored in this study extend beyond veterinary medicine to encompass broader human health concerns. There are remarkable parallels between the subtypes of lymphoproliferative disorders in animals and humans, particularly Hodgkin’s lymphoma and non-Hodgkin’s lymphoma. Understanding the etiology of a cancer of the lymphatic system formation is critical for developing both preventive strategies and therapeutic interventions, with the potential to significantly improve patient outcomes. The aim of this study is to discuss the optimal composition of the microbiome in dogs and cats and the potential alterations in the microbiota during the development of intestinal lesions, particularly intestinal lymphoma. Molecular and cellular analyses are also incorporated to detect inflammatory changes and carcinogenesis. A review of the literature on the connections between the gut microbiome and the development of lymphomas in dogs and cats is presented, along with potential diagnostic approaches for these cancers.