In this work, characterization of the botanical origin of honey was carried out using headspace gas chromatography coupled to ion mobility spectrometry (HS-GC-IMS). The proposed methodology was applied for the analysis of 89 samples from ten different botanical origins. A total of 15 volatile compounds could be identified, namely, 3-methyl-1-butanol, heptanal, valeraldehyde, octanal, trans-2-hexenal, nonanal, hexanal, benzaldehyde, 2-heptanone, 2-butanone, 2-hexanone, 6-methyl-5-hepten-2-one, 2-pentanone, ethyl acetate and linalool. The analytical method was characterized in terms of limits of detection and quantification, and precision, in order to quantify the identified compounds. Compounds were quantified using the sum of the protonated monomer and proton-bound dimer and logarithmic regression (R2 > 0.98), although the establishment of a concentration threshold that would allow creation of classification rules was not possible since there was variability within the group. Consequently, the establishment of chemometric models was necessary. A non-targeted strategy using 275 features is proposed. Orthogonal partial least squares-discriminant analysis (OPLS-DA) allowed the differentiation of five botanical origins: thousand flowers, rosemary, albaida, orange blossom, and "others" (rest of the investigated botanical origins, since a limited number of samples was available). A success validation rate of 100% allowed the classification of 14 honeys with unknown botanical origin.