There is an increasing incidence in non-communicable diseases (NCD) such as obesity, diabetes and metabolic syndrome all over the world, despite of the governmental investments in healthy policies. Some of these diseases represent a high economic burden to individuals and society, demanding urgency in the identification of risk factors and appropriate solutions. Inadequate nutrition habits are an important risk factor for developing these diseases, and the consumption of functional foods such as prebiotics, probiotics, and phenolic compounds may contribute to mitigate them. It has been reported that the consumption of prebiotics can cause positive changes in the intestinal microbiota. The healthy microbiota, consisting mainly of Bifidobacterium and Lactobacillus, ferment prebiotics producing compounds that appear to play a protective role against metabolic diseases. Despite the growing number of publications on the effects of regular consumption of prebiotics in experimental models, additional studies on their effects on humans are needed to bring more subsidies to public health programs. This manuscript aims to review the literature on the possible benefits of ingestion of prebiotics in the control of obesity.