Main conclusionA multi-year study of perennialZ. dumosumshows a consistent seasonal pattern in the changes of petiole metabolism, involving mainly organic acids, polyols, phenylpropanoids, sulfate conjugates, and piperazines.AbstractGC–MS and UPLC–QTOF-MS-based metabolite profiling was performed on the petioles of the perennial desert shrubZygophyllum dumosum Boiss(Zygophyllaceae). The petioles, which are physiologically functional throughout the year and, thus, exposed to seasonal rhythms, were collected every month for 3 years from their natural ecosystem on a southeast-facing slope. Results showed a clear multi-year pattern following seasonal successions, despite different climate conditions, i.e., rainy and drought years, throughout the research period. The metabolic pattern of change encompassed an increase in the central metabolites, including most polyols, e.g., stress-related D-pinitol, organic and sugar acids, and in the dominant specialized metabolites, which were tentatively identified as sulfate, flavonoid, and piperazine conjugates during the summer–autumn period, while significantly high levels of free amino acids were detected during the winter–spring period. In parallel, the levels of most sugars (including glucose and fructose) increased in the petioles at the flowering stage at the beginning of the spring, while most of the di- and tri-saccharides accumulated at the beginning of seed development (May–June). Analysis of the conserved seasonal metabolite pattern of change shows that metabolic events are mostly related to the stage of plant development and its interaction with the environment and less to environmental conditions per se.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00425-023-04168-2.