Our contribution adds important new insight to the recent finding that polyoxometalate catalysts, such as H8PV5Mo7O40 (HPA‐5), are very effective catalysts in the extractive oxidative desulfurization of fuels using molecular oxygen. Our contribution focuses on aspects of catalyst stability and deactivation caused by the accumulation of acidic products and intermediates, i. e. sulfuric acid, formic acid, acetic acid, sulfoacetic acid or 2‐sulfobenzoic acid. These compounds reduce the pH value of the aqueous catalyst phase during the course of the desulfurization reaction. At lower pH values, the higher V‐substituted species rearrange to lower V‐substituted species and VO2+. This rearrangement is responsible for a decreasing activity in extractive oxidative desulfurization. We show that formic acid, acetic acid, sulfoacetic acid and 2‐sulfobenzoic acid block active sites of the catalyst. Oxalic acid, in contrast, has been found to exert a remarkable positive effect on catalyst activity. The feasibility of catalyst recycling and efficient isolation of the decomposition products is demonstrated using four commercially available organic solvent nanofiltration membranes.