The prebiotic effect of a food product is characterized by the beneficial physiological outcome that arises from the modulation of the composition and/or activity of the intestinal microbiota through the metabolization of a non-digestible compound. As this is a recent area of research in the coffee field, there are only a few available studies investigating the potential of coffee beverage and by-products (silverskin and spent coffee ground) as an enhancing agent for beneficial microbiota growth. Coffee polysaccharides (galactomannan and type 2 arabinogalactan), melanoidins and chlorogenic acids are the main studied candidate compounds. Results are sometimes controversial but generally indicate positive effects on intestinal microbiota, stimulating the growth of Bifidobacterium spp., Bacteroides-Prevotella group and, in a few studies, also Lactobacillus spp. Among potential benefits, the in vitro production of short chain fatty acids after incubation of human fecal bacteria with coffee has been reported. These studies will be reviewed in the present chapter.