<p>Training system and rootstock influence grape quality by regulating vegetative vigor, canopy structure, and metabolite biosynthesis, which may impact the juice shelf life. This study applied a targeted metabolomics approach to evaluate how combinations of training system and rootstock affect the physicochemical, phenolic, antioxidant, and volatile profiles of ‘BRS Magna’ grape juices during 24 months of storage. The metabolomic evaluation was conducted using LC-DAD-qTOF-MS for phenolic profiling, HS-SPME-GC-qMS for volatile characterization, and spectrophotometric assays to determine antioxidant activity and color. All juices met regulatory standards of total acidity (61.77–75.31 mEq L⁻¹), volatile acidity (1.13 and 1.75 mEq L⁻¹) and soluble solids (16.3–19.2 °Brix) during 24 months of storage. Total acidity and phenolic compounds, especially anthocyanins, declined during storage, causing orange color shifts and reduced antioxidant activity. These changes were observed for all combinations of training systems and rootstocks. However, the espalier × IAC 572 combination resulted in juices with the highest phenolic content, which contributed to greater antioxidant activity and enhanced color stability even after 24 months of storage. These juices also contained higher levels of esters and furaneol, enhancing pleasant aromas compared to other combinations. The enhanced performance of this combination was attributed to greater sunlight exposure and vegetative vigor, which stimulate the biosynthesis of metabolites linked to stability. This study demonstrated that the storage potential of grape juices can be optimized through agronomic practices that promote the accumulation of quality- and stability-related metabolites.</p> Graphical abstract <p></p>