Background Lactic acid bacteria are able to reduce the immunoreactivity of proteins of cereal grains during wheat dough fermentation or may be a source of proteolytic preparations added during bread making. The key enzyme in prolamin degradation is prolyl endopeptidase. This study was aimed at optimizing the composition of a culture medium and culture conditions that would enhance the synthesis of intracellular prolyl endopeptidase (PEP) by Lactobacillus acidophilus 5e2. Results The application of Plackett-Burman screening plans enabled demonstrating that the concentration of a nitrogen source in the culture and the initial pH value of the culture medium were significant for PEP synthesis. Further optimization conducted with the method of central composite designs (CCD) confirmed both the linear and square impact of nitrogen concentration and initial pH value of the culture medium on PEP production. In turn, the response surface method (RSM) allowed determining the optimal nitrogen concentration and pH value at 26.88 g/l and pH 4.85, respectively. Conclusions Validation of the resultant model enabled over 3-fold increase in the quantity of the synthesized enzyme.