<p>This study was designed to valorize dairy byproducts including cheese whey and buttermilk through developing fermented beverages using a novel isolated <i>Apilactobacillus kunkeei</i> EABW06 strain from Egyptian bee’s wax. Cheese whey or buttermilk was fermented with <i>A. kunkeei</i> and compared to fermented whey or buttermilk supplemented with Rutab date pulp on day one or after 15 days of cold storage. Physicochemical, microbiological, sensory, proteolytic, and various functional properties were investigated. Fermented buttermilk beverages particularly supplemented with date pulp had the highest viscosity and water-holding capacity at the beginning or after 15 days of cold storage. The supplementation with date pulp led to increase the viable count of <i>A. kunkeei</i>. Compared to fermented whey beverages, fermented buttermilk beverages recorded the greatest scores of sensory attributes. The proteolytic, ACE-I, and antioxidant activity enhanced in fermented buttermilk supplemented with or without date pulp. A storage period exhibited a positive effect on the proteolysis, ACE-I, and DPPH radical scavenging properties of fermented beverages. All fermented beverages showed a great inhibitory impact against the growth of various species of fungi and bacteria. Fermented buttermilk beverages demonstrated the highest cytotoxicity against Caco2 cell lines with IC₅₀ values of 81.22–86.89 μg/mL. However, fermented whey beverages had the strongest inhibition of α-amylase and α-glucosidase enzymes. These findings propose that whey or buttermilk serves as an effective medium for the growth of <i>A. kunkeei</i> and potentially enabling the development of innovative fermented dairy beverages with beneficial health effects.</p>