The chemical composition and potential prebiotic effects of 4 different flours from varieties of sweet potato roots (SPR), including two with white peel and two with purple peel, cultivated in Northeastern Brazil were studied. SPR flours (SPRF) showed variable contents of soluble (1.8–3.0%) and insoluble (4.6–5.8%) fiber, resistant starch (6.2–10.3%), nystose (not found up to 7.1 g/l), kestose (1.7–5.4 g/l), phenolic compounds (phenolic acids: not found up to 16.9 mg/l, flavanols: not found up to 20.4 mg/l, flavanones: not found up to 26.0 mg/l) and sugars (fructose: 4.6–6.1 g/l, glucose: 5.4–8.7 g/l, maltose: 3.2–27.2 g/l). SPRF (20 g/l) with and without a simulated gastrointestinal digestion had an average positive prebiotic activity score (0.11–0.55) with probiotics Lactobacillus acidophilus, L. casei and Bifidobacterium animalis to the detriment of enteric competitors, showing selective stimulatory effects on beneficial bacteria species that are found as part of the gut microbiota. Cultivation of these probiotics in media with or without simulated digestion (SPRF, 20 g/l) showed high bacterial counts (8.2–9.7 log CFU/ml), decreased pH, increased acetic, formic, lactic, malic, succinic and tartaric acids and decreased fructose, glucose and maltose over time, which are indicative of strong metabolic activity. These results showed that flours from different SPR varieties are potential prebiotic ingredients for use in the formulation of functional foods or dietary supplements.