Indigo carmine (IC) dye is hazardous and allergenic for humans even though it has been excessively used in a wide range of industries. Therefore, the quantitative determination of IC is still challenging. Herein, for the first time, we have developed fluorometric and colorimetric dual-mode nanoprobe derived from the ion-pair association complex between the negatively charged IC and positively charged N@C-dots in pH = 3.0. Consequently, the binding between N@C-dots and IC resulted in cyan blue and quenching of N@C-dots fluorescence. The dependence of the fluorescence response on IC concentrations was linear over the range of 0.73–10.0 µM (R2 = 0.9989) with LOD of 0.24 µM. On the other hand, the linearity of the colorimetric method ranged from 9.97 to 80.0 µM (R2 = 0.9986) with LOD of 3.3 µM. The sensor was applied for estimation of IC in fruit juice and soft drink without the need for exhaustive extraction steps.