Although many fruit by-products are good sources of nutrients, little is known about their prebiotic potential. This research was aimed at establishing the prebiotic effect of pineapple wastes on probiotics including Lactobacillus (L.) acidophilus (ATCC® 4356™), L. casei (ATCC® 393™) and L. paracasei spp. paracasei (ATCC® BAA52™) and the subsequent release of antioxidant and antimutagenic peptides in yogurt during their growth. Oven- and freeze- dried peel and pomace were milled separately into powders and tested for prebiotic activities. The net probiotic growth (1.28–2.14 log cfu/g) in customized MRS broth containing the pineapple powders as a direct carbohydrate source was comparable to MRS broth containing glucose. The powders were also separately added to milk during the manufacturing of yogurt with or without probiotics. An increase (by 0.3–1.4 log cycle) in probiotic populations was observed in the yogurts as a consequence of pineapple powder supplementation. Crude water-soluble peptide extracts, prepared by high-speed centrifugation of the yogurts, displayed remarkable antioxidant activities assessed through in vitro assays, namely scavenging activity of 1,1-diphenyl-2-picrylhydrazyl radicals (IC50 = 0.37–0.19 mg/ml) and hydroxyl radicals (58.52–73.55 %). The peptide extracts also exhibited antimutagenic activities (18.60–32.72 %) as sodium azide inhibitor in the Salmonella mutagenicity test. Together, these results suggest that pineapple by-products exhibited prebiotic properties and could possibly be commercially applied in new functional food formulations.