The bloc is reportedly engulfed by infighting over the system known as “Spitzenkandidat”, which translates as “leading candidate” awards the Commission presidency to the party winning the most seats in Parliament.
Jean-Claude Juncker claimed victory in 2014 using the same process.
But as the EU prepares to say goodbye to Mr Juncker next year, French President Emmanuel Macron and other leaders of nations including, Poland, Portugal, the Czech Republic, Hungary, Lithuania, Slovakia and the Netherlands, have raised concerns over how democratic the current election process is.
Used for the first time in 2014 when Mr Juncker took the top job as the European Commission president, the British prime minister at the time David Cameron and Hungary’s Viktor Organ vehemently opposed the system.
But Mr Junker will today attempt to confront EU member states over their opposition as he backs the European Parliament’s plans to retain and strengthen the Spitzenkandidat system before it is discussed at a summit next week.
In papers seen by the Financial Times, Mr Juncker will say the system has “raised the profile of pan-European electoral campaigns” and helped stem declining voter turn out at EU elections.
Croatia’s prime minister, Andrej Plenković, warned it would be difficult to abandon the Spitzenkandidat system, even though many national governments want to.
He said: “One of the objectives is to have a larger turnout, another one to give bigger legitimacy to the president of the Commission.” He added to achieve that “linking legitimacy plus the support of the European Parliament plus the European Council” is needed.
Denis MacShane, UK’s former minister of Europe, last year branded the process “a symbol for the secretive, undemocratic power plays the EU was supposed to have left behind”.
EU boss Mr Juncker recently admitted he “sensed” the European Council was reluctant to put the process forward ahead of the 2019 European election and he feared “conflict”.
He said: “My sense is that there’s almost a majority against it in Council.
“This is a conflict between political parties and it could lead to a conflict between this house and the European Council.”
He also insisted the system is a “tiny piece of democratic progress”.