The effects of temperature, pH, inoculum level, and NaCl on the growth and metabolism of Lactobacillus sanfranciscensis and Candida humilis in rye sourdough were determined. The temperature optima for growth of C. humilis and L. sanfranciscensis were 28 and 32 °C, respectively. Yeast growth was inhibited at 35 °C. The pH did not affect yeast growth in the range 3.5–5.5, whereas growth of L. sanfranciscensis was inhibited at pH 4.0. A NaCl concentration of 4% (flour base) inhibited growth of L. sanfranciscensis but not C. humilis. The effects of the process parameters on the formation of lactate, acetate, ethanol, and CO2 by the organisms were generally in agreement with their effects on growth. However, decreased formation of acetate by L. sanfranciscensis was observed at 35 °C although lactate and ethanol formation were not affected. In conclusion, the study provides a rationale for the stable persistence of L. sanfranciscensis and C. humilis in traditional sourdoughs and will facilitate the optimisation of sourdough fermentations in traditional and new applications.