It was the morning after the night before. Following a marathon six hours of debate in Brussels, Britain had been granted a Brexit extension to 31 October – an end-date that none of the EU’s leaders’ had wanted.

What had emerged that April evening was a hard-fought compromise between the French president Emmanuel Macron’s demand for a short Brexit delay and the German chancellor Angela Merkel’s wish for the UK to be given a year to think again.

“Everything goes more smoothly when Germany and France are on the same lines, that’s clear,” said one exhausted senior EU official after just a few hours sleep. “This was in the end very much a Franco-German compromise … in the best of the tradition of that relationship.”

Two months on and it is time for another Brussels summit. But it is a change of guard in the EU’s institutions that is the thorny question facing the leaders this Thursday, with Donald Tusk, the European council president, urging swift decisions. “It will be a very dynamic 24 hours,” said a senior EU official.

A batch of EU presidencies are up for grabs, including replacements for Tusk and Jean-Claude Juncker, the outgoing head of the European commission. Other soon-to-be vacant posts include the EU high representative for foreign affairs and security policy aas well presidents of the European Central Bank and parliament.

The distribution of this “package” of roles will take into account geographical representation, sex – there has never been a female commission or council president – and political affiliation.

Despite the insistence of many that viewing the bloc through the prism of a Franco-German engine fails to acknowledge the complexity and democratic foundations of the modern EU decision-making processes, and recent fallouts between Paris and Berlin over Macron’s demands for a eurozone budget and much else, it is France and Germany the institutions appear likely to rely upon for an answer.

Merkel will meet Macron hours ahead of the summit on Thursday lunchtime.

Five years ago, when Juncker was selected, it appeared that the 2009 Lisbon treaty had diluted the prerogative of the national leaders to decide, making the choice of commission president turn on the result of European parliamentary elections.

Leaders needed to reflect the makeup of the elected parliament. The parliament would then need to endorse the nominee.

Juncker was the nominee of the centre-right European People’s party (EPP), the so-called Spitzenkandidaten, with the help of a gang of federalist-leaning MEPs and when the EPP won, the national leaders were caught napping.

The former prime minister of Luxembourg, a candidate for the head of the commission that almost nobody wanted, won.

Most of the main political groups had their Spitzenkandidaten this time too, but the parliament has been left fractured. Not only are the EPP, and the Socialists and Democrats group weakened, and the liberal group, now known as Renew Europe, strengthened, in large part because of the strong showing of the Macron’s En Marche party and Britain’s Liberal Democrats, the Greens have emerged as a significant force.

The difficulty for those parties in coalescing around a common programme has been a barrier to reaching an agreement on who they believe should succeed Juncker.

Tusk’s twin-track attempts to find a compromise, through asking six prime ministers representing the three main parties to hold talks, appears to have failed to find a solutions.

“So the only way to get agreement is if the French and Germans bang their heads together,” said Mujtaba Rahman, from the Eurasia consultancy group.

Merkel has been outspoken in pushing for her compatriot Manfred Weber, the leader of the EPP in the parliament who was the group’s Spitzenkandidat, and a member of the CSU, a sister party to the chancellor’s CDU.

Macron has been equally outspoken in rejecting Weber, who has no government experience. The president’s stance is viewed as part of an larger attempt to break the hold the EPP has on the main EU institutions, where its members occupy all the senior posts. “I am with you,” he recently toldMargrethe Vestager, the competition commissioner and candidate of Renew Europe.

“The Franco-German relationship hasn’t been plain sailing for quite a while so it is not a big surprise that the leaders clash over who will become president,” said Agata Gostyńska-Jakubowska, a senior research fellow at the Centre for European Reform thinktank.

“But it is important for Emmanuel Macron to have his way because at least on eurozone issues it seems back home that he didn’t get what he promised the public when he was running for the presidency.

“The question is does Macron get what he wants, or does Germany and the member states package it so it looks like he has got his way? That is when we get to compromise candidates acceptable to both Berlin and France,” she continued. “What it means, unfortunately for the European project, is that instead of ending up with someone pretty bold on the big challenges we could end up with a candidate who is not as bold as the public would like.”

There is a time impetus. The European parliament will select its president, or speaker, on 2 July. If a figure such as Guy Verhofstadt, the outgoing leader of Renew Europe, were to secure the role, it would present a block to Vestager succeeding Juncker.

“The power struggle between council and parliament has been under-appreciated,” said Guntram Wolff, director of the Brussels-based Bruegel thinktank.

Should Macron be successful in killing off Weber’s chances, and the EPP refuse to endorse anyone else when it comes to a parliamentary vote, there would be paralysis: an institutional crisis that no one wants.

“What is likely to emerge will not be the commission that anyone hoped for,” said one EU diplomat. “It will be the commission that is the least biggest disappointment to everybody.”