As metabolic intermediates, volatile fatty acids (VFAs) can be recovered by separation and purification and contribute to the economy. It was necessary, however, to investigate the optimization of liquid–liquid extraction (LLE) in this study because of the technical difficulties encountered during the recovery of VFAs. For this reason, the organic solvents diethyl ether, trioctylamine, and toluene were investigated as LLE solvents to extract VFAs from Baker’s yeast industry effluent, which contains high levels of organic matter. An optimal pH value of 3 was determined by a pH scan performed between pH 2.5 and pH 7.5. Principal component analysis (PCA) was used to determine the effects of organic solvents and pH on extraction efficiency. The extraction efficiency was evaluated using the optimal pH and multi-stage extraction experiments. In a three-stage extraction, diethyl ether recovered 82% of the VFAs, making it a promising organic solvent for extracting VFAs from anaerobic fermentation broth. PCA revealed that an opposite correlation between VFA recovery and pH for each organic solvent. Based on the results of the cost analysis, it was determined that the costs of recovering VFAs were reduced by 90% per kilogram.