When President Trump issued an executive order in February against the chief prosecutor of the International Criminal Court for investigating Israel for war crimes, Microsoft was suddenly thrust into the middle of a geopolitical fight.

For years, Microsoft had supplied the court — which is based in The Hague in the Netherlands and investigates and prosecutes human rights breaches, genocides and other crimes of international concern — with digital services such as email. Mr. Trump’s order abruptly threw that relationship into disarray by barring U.S. companies from providing services to the prosecutor, Karim Khan.

Soon after, Microsoft, which is based in Redmond, Wash., suspended Mr. Khan’s I.C.C. email account, freezing him out of communications with colleagues just a few months after the court had issued an arrest warrant for Prime Minister Benjamin Netanyahu of Israel for his country’s actions in Gaza.

Microsoft’s swift compliance with Mr. Trump’s order, reported earlier by The Associated Press, shocked policymakers across Europe. It was a wake-up call for a problem far bigger than just one email account, stoking fears that the Trump administration would leverage America’s tech dominance to penalize opponents, even in allied countries like the Netherlands.

“The I.C.C. showed this can happen,” said Bart Groothuis, a former head of cybersecurity for the Dutch Ministry of Defense who is now a member of the European Parliament. “It’s not just fantasy.”

Mr. Groothuis once supported U.S. tech firms but has done a “180-degree flip-flop,” he said. “We have to take steps as Europe to do more for our sovereignty.”