Neonatal puppies and kittens face a critical period after birth, during which their health depends heavily on the microorganisms they acquire from their mothers and environment. These microorganisms, known as the gut microbiota, help newborns develop their immune systems, digest nutrients, and protect against disease. This review explores how these microorganisms are transferred from the mother to her offspring before, during, and after birth, including the process of delivery, nursing, and maternal care. It also examines how factors such as birth type, hygiene, feeding, and maternal health can influence the development of these microbial communities. When this process is disrupted, it may lead to health problems such as infections, diarrhea, and immune disorders. Understanding how and when these microbes are passed to newborns, and how to support this process, is essential to improving survival rates and long-term health in puppies and kittens.