In the present work, non-targeted metabolomics was used to investigate the seed response to kinetin, a phytohormone with potential roles in seed germination, still poorly explored. The aim of this study was to elucidate the metabolic signatures of germination triggered by kinetin and explore changes in metabolome to identify novel vigor/stress hallmarks in Medicago truncatula. Exposure to 0.5 mM kinetin accelerated seed germination but impaired seedling growth. Metabolite composition was investigated in seeds imbibed with water or with 0.5 mM kinetin collected at 2 h and 8 h of imbibition, and at the radicle protrusion stage. According to Principal Component Analysis, inositol pentakisphosphate, agmatine, digalactosylglycerol, inositol hexakisphosphate, and oleoylcholine were the metabolites that mostly contributed to the separation between 2 h, 8 h and radicle protrusion stage, irrespective of the treatment applied. Overall, only 27 metabolites showed significant changes in mean relative contents triggered by kinetin, exclusively at the radicle protrusion stage. The observed metabolite depletion might associate with faster germination or regarded as a stress signature. Results from alkaline comet assay, highlighting the occurrence of DNA damage at this stage of germination, are consistent with the hypothesis that prolonged exposure to kinetin induces stress conditions leading to genotoxic injury.