The use of Cohesion Policy and Common Agricultural Policy funds vary significantly between regions within the European Union. Each policy fund typically benefits different recipients within the same region. While conventional wisdom suggests that there are implications stemming from the overlap in these policy streams within the same region, this study explores the source and the extent to which a synergy or trade-off arises. Using multivariate statistical analysis, this paper models the associations in the allocation of specific EU Cohesion Policy and Common Agricultural Policy funds among spending sub-categories. Results show that this more granular measurement, whilst considering multiple preferences in aggregating structural place-based characteristics by employing the sigma-mu methodology, provides evidence of policy synergy and trade-offs arising within territories. Thus, we identify the specific sources of funding categories that work successfully in tandem and those that seemingly have a detrimental effect when applied simultaneously in the same region. This poses challenging questions about the choice of policy mix for generating positive synergies and whether such a framework can be extended to other policy realms and their interactions