The coordination of the financial instruments of the European Union  is ensured by the Regulation laying down general provisions on the European Regional Development Fund, the European Social Fund and the Cohesion Fund [Regulation 1083/2006]. According to article 9 § 4 of this Regulation, the Commission and the Member States shall ensure the coordination between the assistance from these Funds, the European Agricultural Fund for Rural Development (EAFRD), the European Fisheries Fund (EFF) and the interventions of the EIB and of other existing financial instruments, notably the European Investment Fund (EIF). Such coordination should also cover the preparation of complex financial schemes and public-private partnerships. The Commission is assisted by a Coordination Committee of the Funds set up by Article 103 of the Regulation. In addition, the national strategic reference framework may also contain, the procedure for coordination between the European cohesion policy and the relevant national, sectoral and regional policies of the Member State concerned.

In order to maximise the stimulus provided by the budget resources deployed, making use of appropriate financial instruments, the European assistance provided in the form of grants may be combined in an appropriate way with loans and guarantees of the European Investment Bank (EIB) [see section 7.3.3]. The latter is the longest standing regional development instrument, for the Treaty of Rome called upon it to ensure a balanced and smooth development of the common market in the interests of the Union (Article 309 TFEU, ex Article 267 TEC). Almost 75% of EIB financing in the Union contribute to regional development, although they pursue other objectives such as those of promoting SMEs and trans-European networks [see section 6.8]. The EIB notably supplies long-term capital for the financing of infrastructure projects in the fields of transport, energy and telecommunications.

Article 309 of the Treaty on the functioning of the EU confirms that the loans and guarantees of the EIB will facilitate projects for developing less-developed regions, for modernising or converting undertakings or for developing fresh activities as well as for projects of common interest to several Member States. This Article makes specific reference to the desired interaction between EIB operations and Structural Funds measures, stating that "in carrying out its task, the Bank shall facilitate the financing of investment programmes in conjunction with assistance from the Structural Funds and other Union financial instruments", which concern regions whose development is lagging behind and declining industrial areas. The Bank also plays an active role in the financing of trans-European networks and thus in the implementation of the support instruments financed by the Union budget: interest rate subsidies on its own loans, co-financing of feasibility studies and co-financing of guarantee funds.