With their desired functional and technological properties, whey protein preparations are used in the food industry. In turn, lactic acid fermentation may contribute to release of a wide range of biologically active peptides (BAPs) (known also as bioactive peptides or biopeptides) from whey and milk proteins, which are perceived as potential therapeutic tools and important constituents of personalized food suitable for prevention of many civilization and diet-related diseases. Therefore, the objective of this study was to determine the suitability of new Lb. helveticus strains for production of fermented milk beverages (drinking type) supplemented with whey protein isolate (WPI). Liquid chromatography-high-resolution mass spectrometry (LC-HRMS) was employed to assess if WPI (water solution) might be a suitable precursor for BAPs produced by selected strains of Lb. helveticus. In order to identify the bioactivities of the peptides generated in WPI hydrolysates, the procedures indicated in databases were used. The fermented products differed from each other in some texture parameters, the content of protein, total nitrogen, and non-protein nitrogen, and the proteolysis index, which was dependent on the strain. Strain B734 was found to exhibit technological potential for development of new health-oriented fermented milk beverages with characteristics of functional food. Additionally, it proved to be able to release a wide range of BAPs from WPI with antioxidative, antibacterial, and immuno- and cyto-modulatory effects, as well as ACE (angiotensin-converting enzyme) inhibitory and antihypertensive activities.