The use of food additives in food production is inevitable in this modern world. Although only a safe amount of food additives is approved, their safety has always been questioned. To our knowledge, the effects of food additives on microbiota have not been investigated in a detailed manner in the literature so far. In this review, the effects of artificial sweeteners, sugar alcohols, emulsifiers, food colorants, flavor enhancers, thickeners, anticaking agents, and preservatives on microbiota were reviewed. Even though most of the results illustrated negative outcomes, few of them showed positive effects of food additives on the microbiota. Although it is difficult to obtain exact results due to differences in experimental animals and models, said the findings suggest that nonnutritive synthetic sweeteners may lead to glucose intolerance by affecting microbiota and a part of sugar alcohols show similar effects like probiotics.