What regional factors can explain the heterogeneity in Structural Funds distribution to European Union regions? Past studies have shown that aside from the level of economic development and rates of unemployment, other political, and economic factors systematically explain why certain European Union regions receive greater funding than others, in particular where there is room for bargaining. In this article, a novel theory is posited which argues that the determination of Structural Funds is based on an interaction between a region’s formal institutions (the level of a regional autonomy) and informal institutions (its level of quality of government). In cases of low regional autonomy, member states and European Union level actors prefer to allocate greater levels of Funds to regions with lower quality of government in order to increase cohesion. Yet in cases of high regional autonomy, risks associated with absorption failure in lower capacity regions lead states to strategically allocate greater levels of transfers to regions with higher quality of government. The theory is tested on data for 171 European Union regions for the 2007–2013 budget period. The results show robust empirical support for the theoretical claims.