The aim of this work was to study the influence of process parameters and the starter culture on the characteristics of wheat sourdough by using response surface methodology. Influence of fermentation temperature (16–32°C), ash content of flour (0.6–1.8%), and fermentation time (6–20 hr) were considered as independent factors and their effects were studied in sourdough fermented with Lactobacillus plantarum, L. brevis, Saccharomyces cerevisiae, or with a combination of yeast and lactic acid bacteria. Formation of acidity, free amino acids, and volatile compounds were considered the main responses. A possibility to enhance formation of potential flavor compounds and precursors without excessive acidity formation in wheat sourdoughs was established. The total amount of amino acids increased by 25–50%, depending on the strain and fermentation conditions. The total amount of volatile compounds increased seven‐ to 100‐fold, depending on the strain and fermentation conditions. Sourdough started with S. cerevisiae was an effective way to optimize the amount of volatile compounds without excessive acidity formation in appropriate processing conditions. Ash content of flour and fermentation time were the most significant factors to modify metabolic activity of wheat sourdoughs. Frequent interactions between the studied factors were observed on the formation of acidity, amino acids, and volatile compounds with most of the strains studied. Possibility to improve current industrial fermentation processes and control flavor attributes of breads by using optimized sourdough was established.