This study aimed at investigating bactericide solutions effective on spoilage and pathogenic bacteria while preserving technological bacteria. Two compounds of essential oil (thymol and eugenol), one essential oil of Satureja thymbra and two industrial biocides (PE 270–30, Brillo) were tested on technological strains (Staphylococcus equorum, Staphylococcus succinus and Lactobacillus sakei) grown in monoculture biofilm and on a mixed biofilm of pathogenic bacteria (Staphylococcus aureus, Listeria monocytogenes) and spoilage bacteria (Pseudomonas fragi, Escherichia coli). Biofilm cultures were performed in glass fibre filters for 24 h at 20 °C before application of biocides. Thymol and eugenol had no effect on the mixed biofilm. S. thymbra (2%) was highly effective on spoilage strains (5 log reduction), and S. equorum (4 log reduction) was moderately effective on pathogens (2.3 log reduction) and not effective on S. succinus and L. sakei (0.5 log reduction). PE-270-30 with 10% Na2SO4 decreased spoilage bacteria (5.1 log reduction), maintained the technological bacteria, but did not reduce the pathogens. The disinfectant Brillo (3%) killed all the strains. These results showed the difficulty in obtaining a biocide that is effective in destroying spoilage and pathogenic bacteria while preserving technological bacteria. Essential oils could be a good alternative for eradicating spoilage bacteria in the food environment where they are often found at high levels.