The partnership principle is a key mechanism to promote multilevel policy‐making in the EU and thus a driver of top‐down, horizontal and bottom‐up Europeanisation. It enables subnational governments to participate in Cohesion Policy as well as in other related policy areas and has facilitated the integration of regional and local authorities with the EU's system of governance. Although previous funding periods strengthened the partnership principle, certain caveats have challenged its effective operation. Particularly, in response to crises, centralised decision‐making and the focus on economic recovery have undermined the engagement in multilevel policy‐making. The paper traces how the EU's governance of the 2008 financial crisis and the COVID‐19 pandemic shaped the partnership principle as a driver of Europeanisation and European integration of regional and local government. It demonstrates how reforms introduced as response to crisis have gradually constrained subnational government's participation in EU policy‐making with lasting effects for future programming periods.