Flour naturally contains a variety of yeasts and bacteria.[ When wheat flour comes into contact with water, the naturally occurring enzyme amylase breaks down the starch into the sugars glucose and maltose, which sourdough's natural yeast can metabolize.With sufficient time, temperature, and refreshments with new or fresh dough, the mixture develops a stable culture. This culture will cause a dough to rise. The bacteria ferment starches that the yeast cannot metabolise, and the by-products, chiefly maltose, are metabolised by the yeast, which produces carbon dioxide gas, leavening the dough.

Obtaining a satisfactory rise from sourdough takes longer than a dough leavened with baker's yeast because the yeast in a sourdough is less vigorous. In the presence of lactic acid bacteria, however, some sourdough yeasts have been observed to produce twice the gas of baker's yeast. The acidic conditions in sourdough, along with the bacteria also producing enzymes that break down proteins, result in weaker gluten and may produce a denser finished product.