•A novel ion pairing between IC and N@C-dots was proposed for the first time.•The interaction resulted in cyan blue color and quenching of N@C-dots fluorescence.•The nanoprobe exhibited good sensitivity and selectivity towards IC.•The application of nanoprobe was extended for analysis of IC in beverages. 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.