The New York Times has been accused of centering its 9/11 anniversary coverage on Islamophobia and framing Muslim Americans as the primary victims of the attacks, a portrayal the newspaper has called a disingenuous attempt to incite outrage.

Critics, including NewsBusters executive editor Tim Graham, contend that the Times' reporting on the 25th anniversary of the attacks disproportionately focused on prejudice against Muslims rather than the event itself. One article, headlined "After 9/11, Islamophobia Shaped a Generation of Muslim New Yorkers," noted that "the attacks unleashed a wave of hate, but the years since have seen Muslim Americans’ political and cultural influence grow."

This report highlighted how Muslim New Yorkers organized their communities in response to alleged Islamophobia, leading to increased political and cultural influence, including the election of the city's first Muslim mayor, Zohran Mamdani. The Times' reporting suggested that Muslim Americans faced a "quarter-century of suspicion and hostility" and have been "scarred by heavy-handed law enforcement tactics and the suspicion, if not outright hostility, of classmates, co-workers, elected officials and cable news commentators."

Afaf Nasher, executive director of the New York chapter of the Council on American-Islamic Relations, was quoted saying Muslim Americans were "pushed against the wall" and chose political empowerment as a way to push back against prejudice. The Times also pointed to a Pew Research Center survey indicating that some Americans believe Muslims are less patriotic, often citing the 9/11 attacks as the reason, and suggested that public attitudes toward Islam have become more negative since the immediate aftermath of the events.

Graham argued that the Times' coverage lacked opposing viewpoints, focusing instead on "hatred and prejudice from Trump and the Republicans" and presenting a "pro-Muslim gush." He also criticized the paper's framing of any surveillance of Muslims or mosques as prejudice, despite concerns about potential support for terrorism by some individuals or groups.

In response to the criticism, a spokesperson for The New York Times stated that the accusations were a "misleading statement" and a "disingenuous attempt to seek attention and stoke outrage by misrepresenting The New York Times's journalism." The spokesperson asserted that the paper has a long history of reporting on the event and its consequences, offering a "deep and diverse set of journalism reflecting on a globally significant event."

The Times published a second story on Islamophobia titled "Facing Islamophobia, Mamdani Keeps Focus on 9/11 Victims," further drawing the attention of conservative critics. The coverage comes as the nation observed the anniversary of the attacks that killed 2,977 people in New York City, the Pentagon, and near Shanksville, Pennsylvania.