The Supreme Court decided its most important religious-freedom case in decades yesterday. And President Barack Obama lost, 9-0.

The case, Hosanna-Tabor Lutheran Church and School v. EEOC, concerns whether religious groups should be free from government interference when choosing their religious leaders. For decades, the lower courts have applied a doctrine called the “ministerial exception,” which prohibits the government from using discrimination laws to force religious organizations to hire or fire particular individuals for jobs with important religious functions. All the lower courts agreed that the ministerial exception existed, but there was some variation as to whether employees with only some religious duties were covered — for example, a teacher who teaches religion in the morning and math in the afternoon.

In its first case considering the issue, the unanimous court agreed that the First Amendment prohibits the government from interfering in these types of decisions. The court explained that the First Amendment “protects a religious group’s right to shape its own faith and mission through its appointments” and that such groups are entitled to “control over the selection of those who will personify their beliefs.” The court found that even an employee who has some secular duties (e.g., teaching math) can qualify as a ministerial employee based on her religious functions (e.g., teaching religion, leading worship services, etc.).

On its own terms, the decision is a huge victory for religious groups. Had the government won the case, courts and government bureaucracies would have been in the position to order churches to hire or retain particular individuals in religious positions, even if the religious group no longer wanted them. If anything, the separation of church and state should mean that the government bureaucrats have no business deciding who will preach and teach any religious faith.

But the bigger story of the case is the court’s emphatic rejection of the narrow view of religious liberty offered by the Obama administration. The administration had argued that religious groups had no greater right to pick their leaders than labor unions or social clubs. And it had argued that even an employee whose job includes teaching the faith to children would not be a minister if she also had any secular duties. Of course, as Chief Justice John Roberts remarked at the oral argument, even the Pope would fail that test, as he surely has occasional secular duties as the head of the Vatican state.

In the unanimous decision, the court emphatically and repeatedly rejected the administration’s narrow view of religious liberty. For example, when discussing the government’s argument that churches should just rely on the freedom-of-association rights to choose their own leaders (the way labor unions and social clubs might), the court rejected that argument as “remarkable” and “untenable.” When considering the government’s efforts to narrow who can be considered a minister, the court called the Obama administration’s position “extreme.” At the oral argument, even Justice Elena Kagan — who was appointed by President Obama and previously served as his solicitor general — noted that the government’s narrow view of the First Amendment was an “amazing” position (and not in the good way).

Such an emphatic rejection of the administration’s crabbed view of religious liberty is likely to have broader consequences. The administration has aggressively used its narrow view of religious liberty in other contexts. For example, when issuing recent regulations to require all employers to pay for contraceptives, sterilizations and drugs that likely cause abortions, the administration issued the narrowest conscience clause in history — one that would exclude a Catholic hospital simply because it is willing to serve Jewish patients.

When attempting to explain its historically narrow protection for conscience, the administration echoed its arguments from the Hosanna-Tabor case, saying the clause is only meant to protect a church from being forced to offer the drugs to employees in “certain religious positions.” The administration argued that its clause sought only to protect “the unique relationship between a house of worship and its employees in ministerial positions.” Given the government’s stingy view of who counts as “ministerial,” it is clear the administration does not think the First Amendment provides much protection for religion.

Hopefully, yesterday’s rejection of such a narrow view of religious liberty as “extreme,” “remarkable” and “untenable” will convince the administration to reconsider its approach to religious-freedom issues — and to provide the types of protections for religion that are required by the Constitution and federal law. If not, the president may encounter even more troubles in court on these issues, particularly now that other judges see the Supreme Court emphatically and unanimously rejecting the administration’s extreme position.

Mark Rienzi is a law professor at The Catholic University of America and an attorney with the Becket Fund for Religious Liberty, which represents Hosanna-Tabor Lutheran Church.