Wine ageing represents an important stage during wine production when the final wine composition is formed. In this study, 2020 and 2021 vintage Merlot red wines were subjected to 12-month ageing in a stainless-steel tank, Excellence oak barrels with medium, medium-plus and medium-long toasting, and a Premium oak barrel with medium toasting. The aim was to investigate the influence of different ageing vessels on the main chemical composition, element content, phenolic profile, antioxidant activity, and wine colour during ageing. The results showed that changes in ethanol, total sugars, pH, and density were minimal, mostly not significant. Slight changes in malic and lactic acid concentration occurred due to malolactic fermentation. Statistically, more changes that are significant occurred in the phenolic profile, and they affected the antioxidant activity of the wine. In both wine vintages, anthocyanin content decreased, followed by an increase in polymeric colour. Elements and individual phenolic compounds changed significantly, depending on vessel type, ageing time, wine vintage, and initial concentrations. The PCA biplots of the mentioned compounds showed that vessel type had a significant influence on wine composition, especially after 12 months of ageing. According to the CIELab parameters, a slight colour change occurred in both wine vintages, but this is not visible to the human eye. According to the obtained results, various changes in the phenolic profile of Merlot wine occurred during ageing, which strongly depended on the ageing vessel used, the ageing time, and the initial wine composition.