The human gastrointestinal tract is colonised by a multifaceted and dynamic population of microorganisms consisting of trillions of microbes called the gut microbiota. Through extensive research using animal models and human studies, the significant contributions of gut microbiota to immune and metabolic balance, protection against pathogens, and even neurobehavioural traits have been established. Members of the genus Bifidobacterium are the first bacteria to colonise the intestinal tract in infants, and now it has been proven that they play a positive role in enhancing the host immunity, nutrient absorption, reducing and treating gastrointestinal infections, as well as improving conditions such as diarrhea, constipation, and eczema. Bacterial nanotechnology is a rapidly growing research area with great potential for improvement and the discovery of innovations in new applications of bacteria such as Bifidobacterium. In this review, we provide an up-to-date summary of the relations of nanotechnology with Bifidobacterium in various fields, including bacterial synthesis of nanoparticles, encapsulation of bacteria, bacterial toxicity of nanomaterial, application in the field of cancer targeting, and also the treatment of other diseases such as Alzheimer’s and IBD.