Faced with challenges related to environmental degradation and the growing need for sustainable development, the food sector must look for innovative and ecological production solutions. One of the increasingly popular directions is the zero-waste approach, which limits waste generation and enables its reuse. This research aimed to evaluate selected quality indicators of the lactic acid fermentation process of beverages based on waste from the bakery industry (wheat–rye bread) to determine the optimal fermentation conditions using two strains of lactic acid bacteria: Lacticasibacillus paracasei and Lactiplantibacillus plantarum. Preliminary process optimization was carried out, taking into account the beverage composition, fermentation time, and starting culture. The process evaluation and the selection of the optimal variant were based on the microbiological quality, pH value, and antimicrobial activity of fermented beverages. The results showed that the bread waste may constitute a base for obtaining fermented beverages as evidenced by the high number of lactic acid bacteria, above 10⁸ CFU/mL, and low pH values (≤3.5) after the appropriate incubation time. Fermented beverages exhibited antibacterial properties against tested indicator microorganisms, which confirmed their functional properties. The analysis of the obtained results and the adopted assumptions enabled the selection of the most optimal variant—the beverage with ground flaxseed, fermented by L. paracasei for 24 h. The conducted research indicates great potential for lactic acid fermentation in the management of bakery waste to create innovative, sustainable food products with probiotic potential.