This work assesses the potential of multidimensional fluorescence spectroscopy combined with chemometrics for characterization and authentication of Spanish Protected Designation of Origin (PDO) wine vinegars. Seventy-nine vinegars of different categories (aged and sweet) belonging to the Spanish PDOs “Vinagre de Jerez”, “Vinagre de Montilla-Moriles” and “Vinagre de Condado de Huelva”, were analyzed by excitation-emission fluorescence spectroscopy. A visual assessment of fluorescence landscapes pointed out different trends with vinegar categories. PARAllel FACtor analysis (PARAFAC) extracted the potential fluorophores and their values in the PDO vinegars. This information, coupled with different classification methods (Partial Least Square Discrimination Analysis “PLS-DA” and Support Vectors Machines “SVM”), was able to discriminate the wine vinegar category within each PDO, for which SVM models obtained better results (>92% of classification). In each category, SVM also allows the differentiation between PDOs. The proposed methodology could be used as an analysis method for the authentication of Spanish PDO wine vinegars.