The use of various aspects of food processing, including the direct inclusion of nano-additives, are rapidly increasing in the field of nanotechnology to enhance the desired qualities in food production, use and storage. The important role of the human gut microbiota is well understood, including its influence on many physiological functions and its alterations, which play an essential role in various human diseases. Research exploring the effect of engineered and naturally occurring nanoparticles (NPs) in the gastrointestinal tract (GIT) of humans on commensal and pathogenic microorganisms is lacking and scarce. Studies should focus on the complex human gut microbiome when investigating the influence of NPs within a human body. Various materials, such as titanium dioxide, silver, silicon dioxide, iron dioxide and zinc oxide, show great potential in affecting the microbiota and causing clinical disorders including colitis, obesity, and immunological dysfunction. This review reports the influence of such nano- food additives towards the gut microbiota (GM), as well as methods to track and monitor the NPsin vivousing techniques such as electron microscopy after interaction with NPs andin vitrogut models currently used to examine the influence of NPs with GM, as well as their limitations.