The successful upscaling of anaerobic fermentation (AF) still relies on ensuring the stable production of volatile fatty acids (VFAs) in high concentrations and yields. The unforeseen events taking place at industrial scale can compromise the AF stability, thereby decreasing the cost-effectiveness of the process. To assess process stability against disturbances and identify AF failure indicators, this investigation explored the effect of starvation and pH control failure in a continuous reactor. The starvation disturbance did not affect AF performance and methanogenesis was not restored, confirming the relevance of selecting proper conditions (25 °C and pH 6.5) to ensure methanogenesis suppression. By contrast, the uncontrolled pH provoked a pH drop to 4.5, limiting the acidogenesis metabolisms and modifying the metabolites profile due to microbiome reshape. Lactobacillus, and members of Lactobacillaceae, Lactobacillales, and Bifidobacteriaceae dominated the microbiome in the pH disturbance, revealing lactic, succinic and oxalic acids as warning indicators of the acidogenesis failure. Nevertheless, the AF was completely recovered after the disturbances evidencing the microbiome robustness against pH range between 4.5 and 5.