Agroindustrial by-products derived from fruit processing are an important source of biocompounds that can be used as functional food ingredients. The objective of this work was to evaluate cactus pear and pineapple peel flours as an alternative carbon source during fermentation using bacteria with probiotic potential. The total fibre content of both flours was over 60%, with total soluble carbohydrate content around 20%, indicating a good carbon source for lactic acid bacteria. Kinetic parameters indicate that peel flours are a suitable carbon source because the lactic acid bacteria grow (mean growth rate constant, k, values close to glucose, 1.52 h) and acidify the culture media (maximum acidification rate, Vmax, approximately 1.60 pH × 10−3 min−1). There was no difference in prebiotic potential or prebiotic activity score for both the peel flours. Pediococcus pentosaceus performs better during fermentation. In this respect, cactus pear and pineapple peel flours can be used as functional ingredients due to their fermentable properties.