Jujube (Ziziphus jujuba Mill.) is a valuable medicinal plant belonging to the family Rhamnaceae. Owing to its rich content of vitamins, pectin, alkaloids, phenolic compounds, and fatty acids, it is of considerable importance in the pharmaceutical industry. Despite the economic and medicinal significance of jujube, information on the diversity of its chemical profile and variations in fruit metabolite composition among different populations in Iran remains limited. In the present study, the chemical profiles of 11 jujube populations collected from eight provinces of Iran were investigated and compared using gas chromatography–mass spectrometry (GC–MS). The obtained data were evaluated using multivariate statistical methods and bioinformatics analyses to determine the patterns of similarity and differentiation among populations based on their chemical composition. The results were evaluated using multivariate statistical and chemometric analyses. Analysis of the GC–MS results revealed significant differences in the chemical composition of fruits among different regions. Based on the similarities and differences in their chemical compositions, the geographical populations were classified into two distinct clusters using Ward's hierarchical clustering method. The results of this study demonstrated that comparing the chemical profiles of different jujube populations can provide valuable information on the metabolic diversity of this species and may contribute to the identification of germplasm resources, the selection of superior populations, and breeding and conservation programs.