Current trends and changing consumer needs indicate a great opportunity for innovations and developments in functional beverages. Scientific and clinical evidence is also mounting to corroborate the consumer perception of health from healthy beverages. So, the aim of this study was to develop probiotic cheese whey or milk permeate-based beverages fermented by 1.0% Lactobacillus acidophilus or L. paracasei and enriched with10% papaya pulp (as prebiotic) and 1.0% stevia leaves extract (as natural sweetener). Four fermented probiotic whey and four milk permeate-based beverages were prepared and investigated for probiotic microbial counts, pH values, titratable acidity and sensorial attributes during storage period at 5±1°C for 10 days. Results of pH values and titratable acidity of the beverages indicated no significant differences between the whey or permeate beverages. However, functional permeate beverages containing stevia extract had slightly higher probiotic viability than whey beverages during cooled storage. Fermented permeate-based beverages were appraised with relatively high overall score over the whey-based beverages. The final beverages were characterized with good sensory properties and a highly viable count of probiotic <10⁸ cfu/mL during 10 days of cooled storage. So, it is strongly advised to produce such a healthy probiotic whey or permeate beverages which fortified by papaya pulp and sweeted with stevia leaves extract.