Abstract The effects of organic acids (lactic and acetic) and extracellular pH (pHex) on the intracellular pH (pHi) of Saccharomyces cerevisiae and Candida milleri during co-fermentation with lactobacilli were investigated by using Fluorescence-Ratio-Imaging-Microscopy (FRIM). Yeasts were grown in a system that partially mimics sourdough composition, using individual fermentation and combinations with lactic acid bacteria. Fermentations were carried out at 25 °C for 22 h at an initial pH of 5.3. The two yeast species grew equally well during the co-fermentations with lactobacilli. Our results reveal large differences in pHi values between the two yeast species, primarily in relation with pHex changes, while the concentration of organic acids did not seem to affect the pHi. Moreover, the pHi of S. cerevisiae seemed to be affected by maltose consumption. The pH gradient (difference between internal and external pH) of S. cerevisiae remained rather constant, ranging from 2.0 to 2.5. C. milleri instead exhibited a higher pHi, that remained constant throughout the experiments and was unaffected by pHex and/or sugar consumption. Thus, the pH gradient of C. milleri varied much more than that of S. cerevisiae, ranging from 2.3 to 3.8. Our results suggest that the two yeast species have different pHi regulation mechanisms.