A Syrah red wine ageing experiment was set up during 24-months and the influence of four micro-agglomerated corks were investigated. Specific phenolic ageing markers were selected and hemi-synthesized: vitisin B, malvidin-ethyl-catechin, and epicatechin-sulfonate. A targeted quantification method of these markers was then developed and validated by using ultra-high performance liquid chromatography - triple quadrupole mass spectrometry (UHPLC-QqQ-MS) operating in MRM (Multiple Reaction Monitoring). Results showed a significant decline in native grape polyphenol levels (anthocyanins, flavanols) as ageing progresses while pyranoanthocyanins, ethyl-linked pigments, and flavanol-sulfonates content increased. The cork oxygen transfer rate emerged as a pivotal factor and had significant effects on polyphenolic concentration evolution but had no significant impact on flavanol-sulfonate formation. These results provide valuable insights into the chemical evolution ongoing during wine ageing, accentuating the pivotal role of cork stopper selection in preserving wine quality over time.