The complaint was filed by opponents of the currently stalled EU-US trade treaty (TTIP) and the EU-Canada agreement, known as CETA, which has now been approved.
A petition calling for both TTIP and CETA to be scrapped was filed to the ECJ, the EU's highest court, in November 2014 after the Commission rejected the ECI petition.
The complainants then went on to collect some 3.2 million signatures and, in doing so, crossed the required quorum in 23 member states.
RELATED CONTENT
The 3.2 million who signed the petition is nearly double the signatures of the most successful ECI to date.
The ECI is an initiative launched by the Commission to encourage citizens to help shape EU policy. The Commission recently announced a wide ranging review of the scheme.
The ECI - 'Stop TTIP' - which is now subject of the ECJ ruling - asked the EU not to conclude TTIP and CETA.
The Greens/EFA group in Parliament say that the Commission's legal arguments in such cases could "immensely limit" ECI in general because the group says the executive wants them limited to concluded treaties only.
German Greens MEP Sven Giegold, Parliament's rapporteur on transparency, accountability and integrity in the EU institutions, said the ECJ ruling on Wednesday is an opportunity to revive the flagging ECI scheme which has been widely criticised as being ineffectual.
Speaking ahead of the ruling, he commented, "The EU judges can breathe new life into the ECI. Europe must offer its citizens more such opportunities for direct participation in EU decision making."
The deputy added, "More than three million EU citizens signed the ECI, 'Stop TTIP', to have their say on EU trade policy. A ruling in favour of this ECI could prove that citizens can truly influence EU decisions even where it hurts powerful interests."
He said that the Commission's original rejection of the 'Stop TTIP' ECI "on the contrary excluded citizens from important European decisions affecting their public services, their health and environment."
The MEP warned that rejecting the complaint or mounting legal challenges against such complaints "could profoundly disillusion citizens about European democracy. Allowing a say by citizens only when it is too late or fits with Commission's agenda would water down the potentially powerful antidote to populist narratives to homeopathic levels.
"We Greens stand by our demand to the Commission to clarify that the scope of ECIs should include mandates for international treaties such as TTIP and CETA as well as proposals for treaty changes. The revision of ECI regulation, as promised by Vice-President Frans Timmermans on 11 April, should include those clarifications."