Using the whole‐vacuolar mode of the patch clamp technique, we studied the effect of the chaotropic anions thiocyanate and nitrate on the electric currents generated by the proton pumping tonoplast ATPase and pyrophosphatase (PPiase), respectively, in vacuoles from suspension cells of Chenopodium rubrum L. Addition of KNO3 (150–250 mM) or KSCN (70–150 mM), and ATP (5 mM, obligatory) irreversibly inhibited the subsequent electric current through the tonoplast ATPase driven by 1 mM ATP, whereas PPiase‐activity by 50 μM PPi remained unaffected. The kinetics of inhibition, indicative of ATPase disintegration by the chaotropic anions, follows a single exponential (τ= 3.44 min). However, apparent ATPase disintegration did not measurably increase the tonoplast conductance. We conclude that, by contrast to organellar F‐ATPases, upon disintegration the transmembrane proteolipid of the V‐ATPase does not act as a proton conductor which, in the presence of chaotropic anions, like chloride or nitrate, would severely perturb solute compartmentation in the plant cell.