Then there were the Dutch.

Riding a wave of euroskeptic fervor that was sweeping the Continent, populists in the Netherlands used the prospect of closer ties with Ukraine to highlight what they characterized as the folly of European Union policies. Europe, they said, was needlessly becoming entwined with a deeply corrupt, economic basket case already in a state of conflict, and Dutch taxpayers would find themselves on the hook.

The populists gathered enough momentum to force a national referendum, which they won in April 2016 with a low turnout.

Even though that vote was nonbinding, Prime Minister Mark Rutte was forced to seek written assurances from other European leaders to help ensure passage through his country’s Parliament and to placate voters who had opposed the agreement.

Among those assurances: The pact does not make Ukraine a candidate to join the European Union, and it does not commit the bloc to come to Ukraine’s defense.

Even so, the referendum left a poisonous legacy.

“The campaign added up to a hugely effective attack on the E.U. that led to the agreement being halted for months and made the Netherlands look very bad — and, for a while, it even looked as if the deal wouldn’t make it, and that would have been the ultimate foreign policy victory for Russia,” said Sijbren de Jong, an analyst at The Hague Center for Strategic Studies.

For committed Europeans like Mr. Juncker, the Dutch vote signals the new state of affairs on the Continent. Populism, for now, seems to have peaked, and Russian meddling is no longer a secret. One of Europe’s most important foreign policy priorities — to draw in former Soviet republics and set them on a path toward adoption of Western political and economic standards — is bruised but intact.

Mr. Juncker said on Tuesday that he wanted the deal to be finalized in time for a summit meeting in mid-July between the European Union and Ukraine.