There is an increasing interest in food science for high-quality natural products with a distinct geographical origin, such as saffron. In this work, the excitation-emission matrix (EEM) and synchronous fluorescence were used for the first time to geographically discriminate between Moroccan saffron from Taroudant, Ouarzazate, and Azilal. Moreover, to differentiate between Afghan, Iranian, and Moroccan saffron, a unique fingerprint was assigned to each sample by visualizing the EEM physiognomy. Moreover, principal component analysis (LDA) and linear discriminant analysis (LDA) were successfully applied to classify the synchronous spectra of samples. High fluorescence intensities were registered for Ouarzazate and Taroudant saffron. Yet, the Azilal saffron was distinguished by its low intensities. Furthermore, Moroccan, Afghan, and Iranian saffron were correctly assigned to their origins using PCA and LDA for different offsets (Δλ) (20–250 nm) such that the difference in the fluorescence composition of the three countries’ saffron was registered in the following excitation/emission ranges: 250–325 nm/300–480 nm and 360–425 nm/500–550 nm. These regions are characterized by the high polyphenolic content of Moroccan saffron and the important composition of Afghan saffron, including vitamins and terpenoids. However, weak intensities of these compounds were found in Iranian saffron. Furthermore, a substantial explained variance (97–100% for PC1and PC2) and an important classification rate (70–90%) were achieved. Thus, the non-destructive applied methodology of discrimination was rapid, straightforward, reliable, and accurate.