Live beneficial probiotic bacteria are often supplemented into foods and beverages to provide putative health benefits. To ensure their beneficial effects, these organisms must survive processing and storage of food, its passage through the upper gastrointestinal tract (GIT), and subsequent chemical ingestion processes until they reach their target organ. However, there is considerable loss in viability of probiotic bacteria during shelf life before use and in the acidic conditions of the stomach and the high bile concentration in the small intestine. Bacillus subtilis, a spore-forming non-pathogenic bacterium, recently has gained interest in its probiotic properties; it effectively can maintain a favorable balance of microflora in the GIT. In addition, B. subtilis produces a robust extracellular matrix that protects it from stressful environments. We thus hypothesized that the extracellular matrix produced by B. subtilis could protect other probiotic bacteria and therefore potentially could be used as a vehicle for delivering viable probiotic cells to humans. Subsequently, we have developed a novel cultivation system that enables co-culturing of B. subtilis along with probiotic lactic acid bacteria (LAB) by increasing production of the extracellular matrix by B. subtilis cells. Moreover, we showed that B. subtilis improved survivability of LAB following desiccation treatment. Since beneficial bacteria are often subjected to freeze-drying during preparation of probiotic substances for their long-term storage, a raised survivability of the bacteria is desirable through drying processes. Our findings indicate that probiotics cells grown in co-culture biofilm with B. subtilis were much more protected under desiccation treatment resulted in increase of up to 3 Log CFU/mL in their viability. Consequently, we believe that the results of our study will provide a novel approach of using a natural system for protection of probiotic bacteria during desiccation and freeze-drying processes.