Fruit by-products are good resources of carbohydrates, proteins, vitamins, and minerals, which may function as growth nutrients for probiotic bacteria. This research aimed at evaluating effects of pineapple peel powder addition on the viability and activity of Lactobacillus acidophilus (ATCC 4356), Lactobacillus casei (ATCC393), and Lactobacillus paracasei ssp. paracasei (ATCC BAA52) in yogurts throughout storage at 4°C for 28d. Plain and probiotic yogurts supplemented with or without pineapple peel powder or inulin were prepared. The probiotic counts in supplemented yogurts at 28d of storage ranged from 7.68 and 8.03 log cfu/g, one log cycle higher compared with nonsupplemented control yogurt. Degree of proteolysis in synbiotic yogurts was significantly higher than plain yogurts and increased substantially during storage. Crude water-soluble peptide extract of the probiotic yogurt with peel possessed stronger antimutagenic and antioxidant activities [evaluated measuring reducing power and scavenging capacity of 1,1-diphenyl-2-picrylhydrazyl; 2,2’-azino-bis(3-ethyl benzothiazoline-6-sulfonic acid), and hydroxyl radicals] than control and maintained during storage. Pineapple peel, a by-product of juice production, could be proposed as a prebiotic ingredient in the manufacture of yogurts with enhanced nutrition, and functionality.