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European sea bass (Dicentrarchus labrax L.) is one of the most economically important fish species in the Mediterranean Sea area. Despite strict requirements regarding indications of production method (wild/farmed), incorrect labelling of sea bass is a practice still frequently detected. The aim of this study was to evaluate the capabilities of two techniques, Near-InfraRed (NIR) spectroscopy and mass spectrometry, to discriminate sea bass according to the production method. Two categories were discriminated based on the docosahexaenoic and arachidonic fatty acid ratio by using a Direct Sample Analysis (DSA) system integrated with a time-of-flight (TOF) mass spectrometer. The cut-off value of 3.42, of fatty acid ratio, was able to discriminate between the two types of fish with sensitivity and specificity of 100%. It was possible to classify fish production by using multivariate analysis with portable NIR. The results achieved by the developed validation models suggest that this approach is able to distinguish the two product categories with high sensitivity (100%) and specificity (90%). The results obtained from this study highlight the potential application of two easy, fast, and accurate screening methods to detect fraud in commercial sea bass production.