The interpretation of the principle of separation of powers in the EU has assumed specific character through the principle of institutional balance. The Court of justice (CJEU) has been playing a leading role in the assessment and oversight of the principle. This paper aims to analyse how the EU interpretation of the principle of separation of powers has shaped the functioning of the EU administrative branch. It focuses on how the CJEU has interpreted the principle of institutional balance through the so-called non-delegation doctrine limiting the delegation of powers to the administration. I argue that the principle has not contributed to framing the accountability of the EU administrative branch.