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.”

Some at the I.C.C. are now using Proton, a Swiss company that provides encrypted email services, three people with knowledge of the communications said.

Microsoft said the decision to suspend Mr. Khan’s email had been made in consultation with the I.C.C. The company said it had since enacted policy changes that had been in the works before the episode to protect customers in similar geopolitical situations in the future. When the Trump administration sanctioned four additional I.C.C. judges this month, their email accounts were not suspended, the company said.

Brad Smith, Microsoft’s president, said the concerns raised by the I.C.C. episode were a “symptom” of a larger erosion of trust between the United States and Europe. “The I.C.C. issue added fuel to a fire that was already burning,” he said.

Mr. Khan has been on leave from the I.C.C. since last month, pending a sexual misconduct investigation. He has denied the allegations.

An I.C.C. spokesman said it was taking steps to “mitigate risks which may affect the court’s personnel” and “taking extensive measures to ensure the continuity of all relevant operations and services in the face of sanctions.”

The episode has set off alarms across Europe about how dependent European governments, businesses and citizens are on American tech companies like Microsoft for essential digital infrastructure — and how hard it will be to disentangle themselves. Concerns about how else Mr. Trump might leverage technology for political advantage has jump-started efforts across the region to develop alternatives.

Casper Klynge, a former Danish and European Union diplomat who worked for Microsoft, said the episode was in many ways the “smoking gun that many Europeans had been looking for.”

“If the U.S. administration goes after certain organizations, countries or individuals, the fear is American companies are obligated to comply,” said Mr. Klynge, who now works for a cybersecurity company. “It’s had a profound impact.”

The tech debate adds to an increasingly fractious U.S.-European relationship over trade, tariffs and the war in Ukraine. Mr. Trump and Vice President JD Vance have criticized how Europe regulates American tech companies, and U.S. officials have made digital oversight and taxation part of ongoing trade negotiations.

European regulators have argued that they need to be able to police the biggest digital platforms in their own countries without worrying that they will face political pressure and punishment from a foreign government.

“If we don’t build adequate capacity within Europe, then we won’t be able to make political choices anymore,” said Alexandra Geese, a member of the European Parliament.

Since Edward Snowden’s leak of scores of documents in 2013 detailing widespread American surveillance of digital communications, Europeans have sought to diminish their reliance on U.S. tech. Lawmakers and regulators have targeted Apple, Meta, Google and others for anticompetitive business practices, privacy-invading services, and the spread of disinformation and other divisive content.

Yet without viable alternatives, institutions across the region have turned to American digital services. Amazon, Google, Microsoft and other U.S. firms control more than 70 percent of the cloud computing market in Europe, which is the essential way for storing files, retrieving data and running other programs, according to Synergy Research Group.

The I.C.C. has been a longtime customer of Microsoft, which provides the court with services like the Office software suite and software for evidence analysis and file storage, according to an I.C.C. lawyer who declined to be identified discussing internal procedures. Microsoft has also provided cybersecurity software to help the court withstand digital attacks from adversaries like Russia, which is being investigated for war crimes in Ukraine.

In February, after Mr. Trump issued penalties against Mr. Khan, Microsoft met with I.C.C. officials to decide how to respond. They concluded that Microsoft’s broader work for the court could continue but that Mr. Khan’s email should be suspended. He switched his correspondence to another email account, said a person who has communicated with him.

Sara Elizabeth Dill, a lawyer who specializes in sanctions compliance, said the Trump administration was increasingly using sanctions and executive orders to target international institutions, universities and other organizations, forcing companies to make hard choices about how to comply.

“This is a quagmire and places these corporations in a very difficult position,” she said. How tech companies with global services respond is especially important, she added, “as the broad repercussions are what people and organizations are primarily worried about.”

Microsoft and other U.S. companies have sought to reassure European customers. On Monday, Satya Nadella, Microsoft’s chief executive, visited the Netherlands and announced new “sovereign solutions” for European institutions, including legal and data security protections for “a time of geopolitical volatility.” Amazon and Google have also announced policies aimed at European customers.

Still, many institutions are exploring alternatives. In the Netherlands, the “subject of digital autonomy and sovereignty has the full attention of the central government,” Eddie van Marum, the state secretary of digitalization in the Ministry of Interior Affairs, said in a statement. The country is working with European providers on new solutions, he said.

In Denmark, the digital ministry is testing alternatives to Microsoft Office. In Germany, the northern state of Schleswig-Holstein is also taking steps to cut its use of Microsoft.

In the European Union, officials have announced plans to spend billions of euros on new A.I. data centers and cloud computing infrastructure that rely less on U.S. companies. Mr. Groothuis, the Dutch member of the European Parliament, said lawmakers in Brussels were discussing policy changes that would encourage governments to favor buying tech services from E.U.-based companies.

“The situation is not tenable, and we see a big push from European governments to become more independent and more resilient,” said Andy Yen, the chief executive of Proton.

European tech companies see an opportunity to win customers from their American rivals. Cloud service providers like Intermax Group, based in the Netherlands, and Exoscale, based in Switzerland, said they had seen a jump in new business.

“A few years ago, everyone was saying, ‘They’re our trusted partners,’” Ludo Baauw, Intermax’s chief executive, said of U.S. tech companies. “There’s been a radical change.”