Rationale Citrus aurantium L. is a plant belonging to the Rutaceae family, whose extracts are extensively used in weight management products and as thermogenic agents. Here we present two methodologies to analyse the extracts obtained from the peels of Citrus aurantium L. that usually require multiple sample preparation and detection steps. Methods Polar compounds of the crude extract from the peels of Citrus aurantium L. (Rutaceae) were investigated by direct infusion electrospray ionization mass spectrometry (ESI‐MS) and high‐performance thin‐layer chromatography (HPTLC) coupled to desorption electrospray ionization mass spectrometry (DESI‐MS). ESI‐MS was performed in both positive and negative ion modes. Molecular imaging of the HPTLC plates was used for the direct analysis of the phytocompounds present in the crude extract from the peels of Citrus aurantium L. by DESI‐MS imaging. Results Characteristic mass spectra with many diagnostic ions were obtained from the extract analysis, allowing a fast and reliable identification of these species. Tandem mass spectrometry (MS/MS) was employed to confirm the identity of specific metabolites. Conclusions HPTLC/DESI‐MS imaging is a relatively fast, versatile, and efficient technique for natural product analysis, since many more ions are observed than with the direct infusion ESI‐MS. The MS/MS technique provided information about the component structures, revealing the presence of important bioactive components. The application of DESI‐MS imaging may contribute to the improvement identification and characterization of pharmacologically active compounds in phytochemistry. Copyright © 2015 John Wiley & Sons, Ltd.