How does party messaging affect voter preferences in European Parliament (EP) elections? As the influence of radical and Eurosceptic parties grows, mainstream parties must choose between driving elite polarisation by directly challenging such positions, or changing the subject. Increased public attention and the need for international cooperation to resolve key political challenges make this an important topic of research, but previous studies have focussed on the national at the expense of the European level. To address this gap, we adopt a longitudinal perspective, combining manifesto and survey data from 2014 to 2024 to calculate EU issue polarization at the political system level, and assess how this conflict moderates the influence of individual-level variables on voter preferences and behaviour in EP elections. Using multi-level regression models, we establish the link between party positions on EU integration, both real and perceived, and voter preferences. We further test this link and find a moderating effect for polarisation at the country level, in particular via an increase in preferences for far-right Eurosceptic parties, with similar links on other issues. However, we do not find these effects simply when the salience of EU integration changes, suggesting that mainstream parties could avoid driving Eurosceptic voting by changing the subject. Our research therefore contributes to an improved understanding of the role of issue positions and issue salience in voter behaviour, with implications for both European and national campaigning.