The outgoing German defence minister will not take office until November, but she already faces a clamour of demands from the factions she will need to unite behind her.
"She gave a very good speech, very pro-European, but the result was disappointing, and the majority very small," former Italian premier Enrico Letta told AFP after Tuesday's vote.
Von der Leyen was nominated to become the first female president of the European Commission by the bloc's 28 national leaders, but backed by only 383 MEPs, a 51 percent majority.
A win, certainly, but far short of the 422 votes her predecessor Jean-Claude Juncker won five years ago, and a weak foundation from which to unite an increasingly fragmented Europe.
Worse, von der Leyen failed to unite the pro-integration centre ground -- Greens boycotted her, along with around a third of the centre-left and many mainstream conservatives.
The parliamentary vote was a secret ballot, but her majority appears to have included eurosceptic Poles, populist Italians and many British MEPs who are due to leave the chamber.
"It could hang over the whole parliamentary mandate. She needs to win over the Greens and the rest of the socialists," said Letta, now president of the Institut Jacques Delors.
- Tough Greens -
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Von der Leyen addressed it in the immediate aftermath of her narrow victory, admitting that many in parliament had been annoyed to see her foisted on them by national leaders.
"There was a great deal of resentment, and I understand it," she said, referring to the manner in which the parliamentary groups' candidates for president were rejected.
But she continued: "I'm very pleased that after just two weeks -- not even two weeks, 13 days -- that we've been able to find a pro-European majority.
"It's a good base to start from, I want to work constructively with this parliament. We need to find answers to overcome the divisions between east and west, north and south."
In her immediate camp, aides were clear-eyed about the chances of expanding her support base. "It's going to be difficult, the Greens are playing hard," one told AFP.
Green group co-president MEP Philippe Lamberts confirmed this, demanding that no less than four members of the commission that von der Leyen will form must come from his party.
"I have reason to think she'll come round to us, it's an untenable situation, there's no majority without the Greens," he said. "If she wants to negotiate, we won't be cheap."
The team forming around von der Leyen knew the vote wold be close, but -- aides said -- they decided to forge ahead "by force" rather than entertain more demands for policy concessions.
On paper, the conservative EPP, socialist S&D and liberal Renew Europe groups could field a comfortable pro-European majority of 444 between them, but on the night many withheld their support.
Von der Leyen will next need their support in October when her team of 27 commissioners -- one from each member state -- is presented to the Strasbourg parliament for approval.
"If she can expand her majority, she'll win," a senior European diplomat told AFP.
But, as another senior envoy added: "If she doesn't secure a stable majority in parliament, we'll have a tough five years."
Other observers are less pessimistic, arguing that resistance to von der Leyen's appointment was mainly due to the way she was chosen and that once in office her agenda would find support.
"A lot of the negatives had nothing to do with her personality or her programme," said Eric Maurice of the Schuman Foundation.
"The election vote isn't automatically indicative of how parliament is going to work."