Carbohydrates play a myriad of critical roles as key intermediaries for energy storage, cell wall constituents, or also fuel for organisms. The deciphering of multiple structural isomers based on the monosaccharides composition (stereoisomers), the type of glycosidic linkages (connectivity) and the anomeric configuration (α and β), remains a major analytical challenging task. The possibility to discriminate 13 underivatized isomeric trisaccharides were reported using electrospray ionization coupled to trapped ion mobility spectrometry (ESI-TIMS). After optimization of scan ratio enhancing both the mobility resolving power (R) and resolution (r), fingerprints from 5 different honeys were obtained. Seven trisaccharides with relative content varying from 1.5 to 58.3%, were identified. It was demonstrated that their relative content and/or their ratio could be used to ascertain origin of the honeys. Moreover, such direct approach constitutes an alternative tool to current longer chromatographic runs, paving the way to a transfer as suitable routine analysis.