The newly developed prediction models, having the aim to classify Romanian honey samples by associating ATR-FTIR spectral data and the statistical method, PLS-DA, led to reliable differentiations among the samples, in terms of botanical and geographical origin and harvesting year. Based on this approach, 105 out of 109 honey samples were correctly attributed, leading to true positive rates of 95% and 97% accuracy for the harvesting differentiation model. For the botanical origin classification, 83% of the investigated samples were correctly predicted, when four honey varieties were simultaneously discriminated. The geographical assessment was achieved in a percentage of 91% for the Transylvanian samples and 85% of those produced in other regions, with overall accuracy of 88% in the cross-validation procedure. The signals, based on which the best classification models were achieved, allowed the identification of the most significant compounds for each performed discrimination.