The safety and quality of post-production residues is essential before they can be reused. Both to explore the possibility of reuse as a fermentation medium and the context of pathogens’ inactivation, the research aimed to characterize the fermentation system ofL. lactisATCC 11454 and brewer’s spent grain, malt and barley, especially to in situ inactivation of selectedBacillusstrains during the fermentation and storage. Barley products were milled, autoclaved, hydrated and fermented withL. lactisATCC 11454. Then, the co-fermentation withBacillusstrains was carried out. The amount of polyphenols in the samples ranged from 483.5 to 718.4 ug GAE g−1and increased after 24 h fermentation withL. lactisATCC 11454. The high viability of LAB in the fermented samples and after 7 days of storage at 4 °C (8 log CFU g−1) indicates the high nutrients bioavailability during the storage. Also, this co-fermentation on different barley products indicated a high reduction level (2 to 4 logs) ofBacillusdue to the biosuppression effect of the LAB strain in this fermentation system. Brewer’s spent grain (BSG) fermented withL. lactisATCC 25 11454 produces a highly effective cell-free supernatant (CFS) for suppressingBacillusstrains. This was evident in both the inhibition zone and fluorescence analysis of bacteria viability. In conclusion, the obtained results justify the use of brewer’s spent grain in selected food products, increasing their safety and nutritional value. This finding is highly beneficial in the sustainable management of post-production residues when current waste material can still serve as a source of food.