The present research study aims to prepare prototypes of beverages from milk permeate (MP) using fermentation with 10 different strains of lactic acid bacteria (LAB) showing antimicrobial properties (L. uvarum LUHS245, L. casei LUHS210, L. curvatus LUHS51, L. plantarum LUHS135, P. acidilactici LUHS29, L. plantarum LUHS122, L. coryniformins LUHS71, L. paracasei LUHS244, P. pentosaceus LUHS183, L. faraginis LUHS206) and MP with (AppMP) or without (MP) the addition of 8% (w/w) apple by-products (App). Two groups of prototypes of beverages were prepared: fermented MP and fermented MP with App (AppMP). Acidity parameters, LAB viable counts, lactose and galactooligosaccharides (GOSs) content, antimicrobial properties against 15 pathogenic and opportunistic bacterial strains, overall acceptability and emotions induced of the final fermented beverages for consumers were evaluated. Results showed that all LAB grew well in MP and LAB strain exhibited a significant (p ≤ 0.05) influence on galactobiose and galactotriose synthesis in the fermentable MP substrate. The highest total content of GOS (26.80 mg/100 mL) was found in MPLUHS29 fermented beverage. In addition, MPLUHS245, MPLUHS210 and AppMPLUHS71 fermented beverages showed high antimicrobial activity, inhibiting 13 out of 15 tested microbial pathogens. The overall acceptability of AppMP fermented beverages was 26.8% higher when compared with fermented beverages without App (MP), and the most intensive “happy” emotion was induced by MPLUHS71, MPLUHS24, MPLUHS183 and MPLUHS206 samples. Finally, very promising results were also attained by the bioconversion of MP with selected LAB and App addition into the prototypes of antimicrobial beverages enriched with GOS.