This study aims to develop nutraceutical beverages containing food processing by-products in their formulation, and determine the opinion of consumers. This is done by testing whether they know that the main ingredients of the product are by-products, performing an overall acceptability test of the developed beverages, and evaluating the emotions induced by the newly developed beverages for consumers. The main ingredients used for the preparation of added-value beverages were fermented milk permeate (containing galactooligosaccharides), extruded and fermented wheat bran (WB) (containing ≥6.0 log10 CFU g−1 viable antimicrobial properties showing lactic acid bacteria (LAB) strains), and different fruit/berry by-products (FBB) (as a source of compounds showing antioxidant properties). The definition of the quantities of bioactive ingredients was based on the overall acceptability of the prepared beverages, as well as on emotions induced in consumers by the tested beverages. Functional properties of the developed beverages were proofed by the evaluation of their antimicrobial and antioxidant properties, as well as viable LAB count during storage. Desirable changes in extruded and fermented WB were obtained: Fermentation reduced sugar concentration and pH in samples with predominant lactic acid isomer L(+). In addition, the viable LAB count in the substrate was higher than 6.0 log10 CFU g−1, and no enterobacteria remained. By comparing the overall acceptability of the beverages enriched with WB, the highest overall acceptability was shown for the samples prepared with 10 g of the extruded and fermented WB (7.9 points). FBB showed desirable antimicrobial activity: Shepherd inhibited—2, sea buckthorn—3, blueberries—5, and raspberries—7 pathogens from the 10 tested. Comparing different beverage groups prepared with different types of FBB, in most cases (except sea buckthorn), by increasing FBB content the beverages overall acceptability was increased, and the highest score (on average, 9.5 points) was obtained for the samples prepared with 5.0 and 7.5 g of blueberries FBB. Moreover, a very strong positive correlation (r = 0.8525) was found between overall acceptability and emotion “happy” induced in consumers by the prepared beverages enriched with extruded and fermented WB and FBB. By comparing the samples prepared with the addition of WB with samples prepared with WB and FBB, it was observed that most FBB increased total phenolic compounds (TPC) content (on average, by 9.0%), except in the case of samples prepared with sea buckthorn. A very high positive correlation (r = 0.9919) was established between TPC and antioxidant activity. Finally, it can be stated that the newly developed nutraceutical beverages were acceptable for consumers, induced positive emotions, and possessed desirable antimicrobial and antioxidant properties, while being prepared in a sustainable and environmentally friendly manner.