Topolin cytokinins have emerged as valuable tools in micropropagation. This study investigates the metabolism of meta-topolin riboside (mTR) in three distinct tree species: Handroanthus guayacan and Tabebuia rosea (Bignoniaceae), and Tectona grandis (Lamiaceae). Employing labeled N15 mTR, we unraveled the complex mechanisms underlying cytokinin homeostasis, identifying N9-glucosylation as the principal deactivation pathway. Our findings demonstrate a capacity in T. rosea and H. guayacan to reposition the hydroxyl group on the cytokinin molecule, a previously unexplored metabolic pathway. Notably, this study reveals remarkable interfamilial and interspecies differences in mTR metabolism, challenging established perspectives on the role of callus tissue in cytokinin storage. These insights not only illuminate the metabolic intricacies of mTR, a cytokinin with interesting applications in plant tissue culture, but also enhances our understanding of cytokinin dynamics in plant systems, thereby enriching the scientific discourse on plant physiology and cytokinin biology.