This paper looks at the financial accountability of Cohesion policy, in particular when financial instruments are used. Financial accountability is ensured by bodies operating at various administrative levels in a ‘single audit’ pyramid. The European Court of Auditors provides the ultimate level of control outside this structure. This paper focuses on the compliance (legality and regularity) and performance dimensions of financial accountability investigated by ECA. In so doing, it assesses whether financial instruments present any distinctive features in these core dimensions. It finds that distinctive performance issues can be identified for financial instruments in Cohesion policy, whereas compliance issues do not vary on the basis of the policy instrument chosen (grants or financial instruments). Other problems emerge from an institutional dimension at EU level.