In this work, we show the control of acidity and chemical reactions in nanofluidic electrochemical reactors with water and organic solvents. We demonstrate the accurate control of the proton concentration using Faradaic cur-rents calibrated against carboxyfluorescein adjusted with external titrations, but also with a tautomer transition occurring at pH 4.2. We deployed our platform for the control of acidity with organic solvents using a modification of the electrodes with a sulfonated tetrafluoroethylene-based membrane, that isolates the acid generating electrodes from the reagents in the solution. This configuration al-lowed us to follow the acidity in the cell using the same carboxyfluorescein, observing no deterioration of the acid/base cycles, proving the effective isolation of the electrodes. Finally, due to the high proton concentration and the acidity contrast between the cell and the outside that can be achieved with our system, we performed the deprotection of acid labile groups in an upstanding glass in a region with 150 μm of diameter. To the best of our knowledge, this plat-form shows the best control of acidity in the smallest volume reported so far.