On Friday, June 28, the United States Supreme Court ruled in a 5 to 4 decision that same-sex couples have the constitutional right to marry. The Court’s ruling overturns restrictions on same-sex marriages in 13 states. While many have celebrated the landmark ruling—which was announced just before last weekend’s gay pride events in cities nationwide—the decision has also sparked concerns about the effect it will have on religious liberty in the United States.

Emma Green at the Atlantic talks about the kind of legal conflicts that are likely to follow from the Court’s decision for gay marriage. These potential conflicts are also addressed in the dissents of justices Samuel Anthony Alito, Jr., John G. Roberts, Jr., Antonin Scalia, and Clarence Thomas.

The question, now, is what will happen to the many, many religious organizations that don’t support homosexuality, let alone gay marriage. This involves everything from stated policies—“for example, [when] a religious college provides married student housing only to opposite-sex married couples,” Roberts writes—to issues of employment and benefits for employees in gay unions.

Religious organizations that discriminate on the basis of sexual orientation are not the only ones likely to face new legal challenges. The dissenting justices also voiced concern about adoption agencies that have religious objections to gay parentage and judges whose faith may now conflict with their institutional role of performing marriages. According to Green, the Court’s decision does not put an end to the debate on same-sex relationships and marriage but only changes its parameters.

The future of gay marriage has long been a question in the United States, and on Friday, the country got an answer. The questions and conversations surrounding gay marriage now will be of a different kind: what it means to oppose, rather than support, same-sex marriage.

A recent article by The New York Times revolved specifically around the question of whether schools and colleges that “forbid sexual intimacy outside heterosexual marriage” and that refuse to extend housing and other services to same-sex partners could soon be denied tax-exempt status. A frequent reference in the current debate is Bob Jones University, which was denied tax exemptions due to its opposition to interracial marriage. During arguments for Obergefell v. Hodges, Justice Alito referred to the 1983 Bob Jones University v. United States decision, asking if opposition to same-sex marriage would follow the same precedent.

University of Virginia law professor Douglas Laycock suggests that Alito and others are overestimating the likelihood of seeing attempts to deny religious schools and institutions tax-exempt status on the basis of their views on homosexuality in the immediate future, saying that only once “gay rights looks like race does today, where you have a handful of crackpots still resisting,” will this become more likely.

David Masci, writing for Pew Research Center, shows that it is neither certain nor inevitable that the ruling will curtail religious liberty and set off further legal cases. As he notes, 13 of the 22 states with laws banning discrimination on the basis of sexual orientation include some level of protection for religious groups.

“There’s a big difference between something that could be an issue and something that’s likely to be an issue,” says Robert Tuttle, who teaches religion and law at George Washington University. Tuttle says he believes there may be some lawsuits, but he predicts that in more cases than not, accommodation and compromise are likely to win out. “After all, we still allow institutions, like universities, to discriminate based on gender,” he says.

But University of Illinois law professor Robin Fretwell Wilson says it’s possible that institutions will be pressured to give ground on gay marriage by federal authorities (such as the Internal Revenue Service, which could take away an institution’s tax-exempt status), state civil rights commissions or private lawsuits.

While some predict “accommodation and compromise,” others echo Tamara Audi’s observation at The Wall Street Journal that “religious organizations are sounding alarm bells regarding the ruling and what it could mean. National Public Radio reports on churches and their congregants who oppose the Court’s ruling viewing it as an infraction of their religious convictions. Some conservative pastors in New Orleans have proclaimed that the “law of the land” cannot change what is “biblically correct.” And dozens of evangelical pastors around the country“—like Jack Hibbs, who “will no longer perform any marriages in his church rather than be pressured to marry same-sex couples”—have enlisted in the American Renewal Project, which aims to “train pastors to become politically active in the public arena to defend what they call biblical values.”

NPR’s Tom Gjelten points out, the Court’s ruling has no direct affect on religious ceremonies. 

In fact, the Supreme Court said ministers who do not approve of same-sex marriages can’t be forced to perform them. The court decision applies only to government functions, not religious ceremonies. But many of those who are now criticizing the court decision don’t recognize that distinction.