The discretionary nature of the EU agencies has spurred debates about the sources of EU agencies’ legitimacy. Within this new executive order, agencies are said to represent a ‘compromise’ reflecting the interests of their multiple principals (the Council, the Commission and even the European Parliament). Accountability mechanisms demand from ‘agents’ to explain and justify their conduct and procedures enabling political, legal, administrative, professional or societal ‘forums’ to pass judgement and thereby add to the legitimacy of democratic governance. The increase in the European Parliament’s powers has led to a situation whereby parliament employs its role in ensuring that the agencies are controlled and held to account. The European Parliament is willing to grant greater powers as long as it contains the possibility to project its own legitimation beliefs and requirements evaluating the legislative accountability in terms of quality of democracy. Using a methodology based on documentary analysis and semi-structured interviews, this paper offers a systematic analysis of the notions that the European Parliament tables via legislative amendments about the appropriate form and level of public control, fair treatment and rights protection when establishing new EU-level agencies.