A comparison between High-Performance Thin-Layer Chromatography (HPTLC) analysis and Liquid Chromatography High Resolution Mass Spectrometry (LC–HRMS), coupled with Principal Component Analysis (PCA) was carried out by performing a combined metabolomics study to discriminate Arbutus unedo (A. unedo) plants. For a rapid digital record of A. unedo extracts (leaves, yellow fruit, and red fruit collected in La Maddalena and Sassari, Sardinia), HPTLC was used. Data were then analysed by PCA with the results of the ability of this technique to discriminate samples. Similarly, extracts were acquired by non-targeted LC–HRMS followed by unsupervised PCA, and then by LC–HRMS (MS) to identify secondary metabolites involved in the differentiation of the samples. As a result, we demonstrated that HPTLC may be applied as a simple and reliable untargeted approach to rapidly discriminate extracts based on tissues and/or geographical origins, while LC–HRMS could be used to identify which metabolites are able to discriminate samples.