Agricultural systems can be seen as nested social-ecological systems. European Union (EU) Member States vary considerably in terms of their agricultural, socio-economic and environmental circumstances. Yet, as participants in the common agricultural market, they are subject to a uniform Common Agricultural Policy (CAP). An important question is whether there is enough room for flexibility to sustain diverse agricultural systems and facilitate national targeting of sustainability-promoting measures. This article analyses the institutional arrangements concerning cross-scale interactions and interdependencies at national and regional (EU) levels, focusing on how Poland and Sweden implement CAP funds in relation to sustainable agriculture, in particular the agri-environmental schemes, for the period 2007-2013. What room is there in practice for accommodating national differences and sustainability priorities offered by the EU agricultural policy, and how are the existing opportunities used by the two countries? It is shown that agri-environmental funds are too small to prevent transition towards large-scale farming in new Member States and CAP does not effectively promote transformation towards sustainable practices in the EU.