Microbial damages caused by biofilm forming bacteria in the dairy industry are a fundamental threat to safety and quality of milk products. Bacillus species, which are common contaminants of dairy products, can form structured multicellular communities known as biofilms on contact surfaces as well as within the milk products themselves. We investigated the role of extracellular matrix (EM) produced through biofilm formation in bacterial survival during milk processing. We used molecular genetics and food microbiology methodology to show that EM, produced by Bacillus subtilis during biofilm formation in milk, have a major role in bacterial survival during the milk processing. Noticeably, the mutant strains of B. subtilis, which cannot produce EM during biofilm formation, showed hypersensitivity to milk processing procedures such as heat pasteurization. This finding indicates that the EM could serve as a protective material for biofilm forming bacteria and un-shielding it would lead to increased sensitivity of bacterial cells to stressful environments encounter during milk processing. Consequently, we aimed to mitigate biofilm formation using the ability of divalent cations such as Mg²⁺ of blocking EM production. Our further findings indicate that in the presence of Mg²⁺ bacterial cells are hypersensitive to the heat pasteurization applied during milk processing. We therefore suggest that un-shielding biofilm forming bacteria of protective EM may provide novel mean to improve dairy products microbial quality.