The Islamic Society of Boston sued The David Project for conspiracy to publish false and defamatory information.

Jacobs led a sustained campaign against the ISB, alleging they had radical ties and had received improper land subsidies from the city.

The Islamic Society of Boston sued Jacobs and The David Project for defamation in 2005; the lawsuit was dropped in 2007.

During his tenure as ADL New England Regional Director, Robert Leikind collaborated with The David Project to create documents alleging terrorist links to Muslim leaders associated with the Islamic Society of Boston's mosque project in the early 2000s. This was part of a broader anti-mosque campaign involving quality-of-life objections and media efforts to oppose the construction, amid allegations of connections to groups like Hamas and Hezbollah. The collaboration contributed to prolonged controversy and opposition to the mosque's development.

Steven A. Cohen, through his organization Americans for Peace and Tolerance (APT), was a primary critic of the Islamic Society of Boston and its Roxbury cultural center. He led CPT/APT campaigns asserting the mosque was led by extremist leaders with ties to Wahhabism and the Muslim Brotherhood, and sought to block public funding and permitting for the facility. As revealed in internal strategy emails released during discovery, he outlined plans to publicize alleged ties between the ISB's leadership and extremist organizations or potential Wahhabi funding sources. Cohen was the subject of extensive investigative reports and litigation initiated by him and his associates, and was a named defendant in ISB's 2006 defamation lawsuit against critics and media outlets, which was later dropped.