The cover story in the January 2004 issue of American Muslims featured an article arguing that "the bible is a distorted document" and that "Zionism began with the Old Testament…Unknown authors willingly distorted the word of God to suit their own self-interest…" The article stated that, "The Middle East conflict today still harkens back to Jews' erroneous claim that God…gave the 'Promised Land' exclusively to Jews."

In July 2003, the online version of the publication, American Muslim Online, featured an article by Omer bin Abdullah called, "Reaching the Roots of Terrorism." Abdullah indicated the history of terrorism began "more than 2,000 years ago," when "Jewish Zealots assassinated their targets, the Roman occupiers, in broad daylight, often in crowded market places or on feast days." Abdullah continued: "The U.S. has placed itself in a corner: It insists that other governments stop, prevent, and even help it to fight terrorism, and yet arms such practitioners of state terrorism as Tel Aviv. Today, terrorism refers to those whom the U.S. dislikes, especially Muslims, or who work against a U.S. ally-of-the-moment."

The May 2003 issue featured a fictional story depicting Israeli soldiers killing Palestinian civilians, describing the soldiers as laughing, their hands covered with blood, as they eat their victims' bread - evoking the anti-Semitic canard of a blood-libel.

In 2002, an issue of American Muslim Online reprinted a fatwa justifying suicide bombings by Fawsal Mawlawi, the radical Lebanese associate of Sheik Yusuf Qaradawi. In the fatwa, Mawlawi explained that "in martyr operations, the Muslim sacrifices his own life for the sake of performing a religious duty, which is Jihad against the enemy."

Some MAS chapters continue to provide anti-Semitic content for their readership. On the MAS Chicago Web site, under the section, "Links of Interest," the organization directs readers toward an article titled, "The Corruption of the Torah."  The author of the article advises this with respect to the Jews: "We should not be so quick to call for death and destruction until all avenues of dawa and calm rational reasoning have been exhausted…Even though Allah (SWT) has told us of the hatred they hide in their hearts, He has not command us to hate and kill every single Jew we meet simply because he is a Jew."

Historically, MAS's Web site also supplied links to movements that espouse extremist ideology and advocate violent jihad.  Available for years until the end of 2002, MAS provided "Islamic Resources" on its Web site, directing its members and visitors to a list of sites including: the Al Manar Web site of Hezbollah, a group designated as a Foreign Terrorist Organization (FTO) by the U.S. Department of State; the Web site of the Yusuf al-Qaradawi; the Moro Islamic Liberation Front; and an Eritrean jihadi movement called the Mujahideen of the Islamic Union in Ogadin.  The MAS resource list also included links to organizations that promote anti-Semitism such as the now-defunct Islamic Association of Palestine (IAP) and Hizb ut-Tahrir.