Purpose Numerous applications of compatible salts (osmolytes) as ectoine in food and pharmaceutical industries have been intensively increased nowadays. Decreasing the cost of industrial production of ectoine using low-cost cultivation media and improving the yield through modeling procedures are the main scopes of the present study. Methods Three statistical design experiments have been successfully applied for screening the parameters affecting the production process, studying the relations among parameters and optimizing the production using response surface methodology. Results A novel semi-synthetic medium based on hydrolyzed corn gluten meal has been developed to cultivate moderate halophilic bacterial strains; Vibrio sp. CS1 and Salinivibrio costicola SH3, and support ectoine synthesis under salinity stress. Two regression equations describe the production process in the new medium have been formulated for each bacterial strain. Response surface optimizer of the central composite model predicts the maximum ectoine production is achieved at incubation time; 63.7 h, pH; 7.47 and salinity; 7.27% for Vibrio sp. CS1 whereas these variables should be adjusted at 56.95 h, 7.089 and 10.34%; on the same order regarding Salinivibrio costicola SH3. In application studies, 50 mu g ectoine decreases RBCs hemolysis due to streptolysin O toxin by 21.7% within ten minutes. In addition, 2% ectoine succeeds to increase the viability of lactic acid bacteria in Yogurt as a classic example of functional food during the storage period (7 days). Conclusion The present study emphasizes on modeling the process of ectoine production by halophilic bacteria as well as its activity as a cryoprotectant agent.