400 MHz nuclear magnetic resonance (NMR) spectroscopy and multivariate data analysis techniques were used in the context of food surveillance to measure 328 honey samples with 1H and 13C NMR. Using principal component analysis (PCA), clusters of honeys from the same botanical origin were observed. The chemical shifts of the principal monosaccharides (glucose and fructose) were found to be mostly responsible for this differentiation. Furthermore, soft independent modeling of class analogy (SIMCA) and partial least squares discriminant analysis (PLS-DA) could be used to automatically classify spectra according to their botanical origin with 95–100% accuracy. Direct quantification of 13 compounds (carbohydrates, aldehydes, aliphatic and aromatic acids) was additionally possible using external calibration curves and applying TSP as internal standard. Hence, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of botanical origin and quantification of selected constituents of honeys.