The characterization and discrimination of chemical compounds is imperative in both academia and industry, but currently relies on expensive and/or bulky instrumentation. Herein, we demonstrate that the ion transport properties of bare quartz nanopipettes containing aprotic acetonitrile electrolyte can be used discriminate isomers based on polarization and solvation, through changes to interfacial solvent ordering at the nanopore wall. This is demonstrated by monitoring the photoinduced isomerization of spirooxazine to merocyanine using the ion-current rectification of a quartz-nanopipette containing acetonitrile electrolyte, which results in an increase in rectification ratio (RR) from 3.6 ± 0.3 to 5.1 ± 0.2. This change is comparable to traditional UV–Vis absorbance and fluorescence measurements of the same process, with the appearance of a small shoulder-like absorbance peak from 400 to 500 nm, and a strong fluorescence signal at 430 nm.