This paper examines whether and how polarisation on the European Union affects voting behaviour in European Parliament (EP) elections. While existing research highlights how EU-related conflict correlates with public attitudes toward European integration, the effects on voting preferences specifically within EP elections remain underexplored. To address this, we adopt a longitudinal perspective, combining manifesto and survey data to calculate EU issue polarization at the political system level, and how this conflict moderates the influence of individual-level variables on voter preferences in EP elections. Building on previous findings that parties often drive EU issue polarization to broaden their appeal beyond the traditional left–right spectrum (De Vries, 2007), we investigate whether EU issue salience affects EP electoral dynamics in different countries. While highly polarised cases such as the UK are well known, we study these effects across a number of countries and elections to identify the nature of these party-voter relationships in a range of contexts. This research contributes to the literature on the politicisation of European integration by clarifying how EU issue polarisation interacts with individual variables, thus enhancing our understanding of its role in shaping voting behaviour in EP elections.