Enterococcus spp. were isolated from sausage and yogurt line production. The genomic assay was performed by PCR, and distinct enterococci (n = 28) were identified. Testing revealed that 10.7% of the isolates had a resistant phenotype, 7.1% were resistant to erythromycin (Enterococcus faecium) and 3.5% were resistant to tetracycline (Enterococcus gallinarum). Enterococci cells and biofilm formation in 24 well polystyrene plates and the effect of sanitisation procedures in these biofilms were determined. The sanitisers were chlorinated alkaline H (CAH), chlorinated alkaline A (CAA), quaternary ammonium D (QAD), quaternary ammonium M (QAM), chlorine dioxide (CD), sodium hypochlorite (SH), and peracetic acid (PA). A total of 7 isolates (25%) moderately and the others poorly formed biofilms. The best reduction results were 61 and 55% of the cells with the CAH sanitiser in BHI and water, respectively. The PAA, SH, and CD sanitisers showed low efficiency on Enterococcus planctonics, and the other had an effect on cell growth. The sanitisers CAH, QAD, QAM, PAA, and SH showed efficiency in reducing the cell viability of Enterococcus in biofilms, and values obtained from CAA and CD suggested low biofilm removal capacity. Enterococcus spp. form biofilms and have become a problem in the food industry.