The use of bacteria and/or their compounds is an alternative to the use of positive-list additives that the food industry is using as a tool to meet consumer demands for more natural, long-shelf-life, and healthy products, in short, to offer clean label foods. The aim of this study is to investigate the suitability of cell-free supernatants (CFSs) from Qualified Presumption of Safety strains as bioprotective cultures. Out of an initial screening panel of about 200 isolates, strains Pediococcus acidilactici CNTA 1059, Lactiplantibacillus plantarum CNTA 600, Levilactobacillus brevis CNTA 1374, and Bacillus subtilis CNTA 517 demonstrated strong antimicrobial activity against, especially, Gram-positive bacteria. The CFSs of these four strains showed minimum inhibitory concentration values between 0.15% and 5% against Listeria monocytogenes and Lentilactobacillus parabuchneri. None of the four selected strains exhibited acquired resistance to target antibiotics, and the non-toxigenicity of all the CFSs was demonstrated. In the case of the three lactic acid bacteria, the presence of bacteriocin-like inhibitory substances was confirmed following the decline in antimicrobial activity due to treatment with proteases. Regarding B. subtilis, biosynthetic gene clusters for different bacteriocin-like substances, including protease-resistant lipoproteins, were found via whole-genome sequencing. In addition, all of the CFSs exhibited stable antimicrobial activity at a wide range of temperatures (70–121 °C) used for the pasteurization and sterilization of food products, with a loss of antimicrobial activity ranging from 3% to 28%. These results point to the possibility that CFSs from these strains could be used in the food industry as a biocontrol tool to develop new products.