The application of 1H and 13C nuclear magnetic resonance (NMR) in conjunction with chemometric methods was applied for the discrimination and authentication of Maltese extra virgin olive oils (EVOOs). A total of 65 extra virgin olive oil samples, consisting of 30 Maltese and 35 foreign samples, were collected and analysed over four harvest seasons between 2013 and 2016. A preliminary examination of 1H NMR spectra using unsupervised principle component analysis (PCA) models revealed no significant clustering reflecting the geographical origin. In comparison, PCA carried out on 13C NMR spectra revealed clustering approximating the geographical origin. The application of supervised methods, namely partial least squares discriminate analysis (PLS-DA) and artificial neural network (ANN), on 1H and 13C NMR spectra proved to be effective in discriminating Maltese and non-Maltese EVOO samples. The application of variable selection methods significantly increased the effectiveness of the different classification models. The application of 13C NMR was found to be more effective in the discrimination of Maltese EVOOs when compared to 1H NMR. Furthermore, results showed that different 1H NMR pulse methods can greatly affect the discrimination of EVOOs. In the case of 1H NMR, the Nuclear Overhauser Effect (NOESY) pulse sequence was more informative when compared to the zg30 pulse sequence, since the latter required extensive spectral manipulation for the models to reach a satisfactory level of discrimination.