Spencer holds the view that "traditional Islam contains violent and supremacist elements," and that "its various schools unanimously teach warfare against and the subjugation of unbelievers." He calls for Muslims to follow an interpretation of Islam that rejects violence and supremacism.. Although he believes Islam has violent elements in its traditional teachings, he rejects the idea that all Muslims must necessarily be violent people as a misunderstanding of his position. Calling attention to the roots and goals of jihad violence. "Any Muslim who renounces violent jihad and dhimmitude is welcome to join in our anti-jihadist efforts. Any hate in my books comes from Muslim sources I quote, not from me. Cries of "hatred" and "bigotry" are effectively used by Muslim advocacy groups to try to stifle the debate about the terrorist threat."
Spencer has expressed strong criticism of the Council on American-Islamic Relations as well as numerous other Muslim advocacy groups, in particular relating to their alleged close ties with jihadist organisations such as the Muslim Brotherhood and their employment of several Muslims who were convicted on charges relating to terrorism.
Spencer says that among moderate Muslims "there are some who are genuinely trying to frame a theory and practice of Islam that will allow for peaceful coexistence with unbelievers as equals," but he also argues that many so-called reformers are not interested in genuine reform, instead aiming to deflect scrutiny of Islam. Spencer feels that anyone pursuing his called-for reforms will face a difficult task, because "the radicals actually do have a stronger theoretical, theological, and legal basis within Islam for what they believe than the moderates do."
His work has been subject to criticism, for its "entrenched hostility" against Islam. His work has been treated dismissively by mainstream scholars, for its alleged mismanagement of basic facts and political activism, while it has been condemned as hate speech by Arab-American and civil rights groups. Spencer responds that criticism of him as Islamophobic is
only a tool used by Islamic apologists to silence criticism. My work is dedicated to identifying the causes of jihad terrorism, which of course lead straight back into the Islamic texts. I have therefore called for reform of those texts... I have dedicated Jihad Watch to defending equality of rights and freedom of conscience for all people. That's Islamophobic? Then is the fault in the phobe, or in the Islam?
In March 2010, Spencer endorsed the far-right English Defence League (EDL), which has been associated with violence and anti-social behaviour, and claims that "The EDL is standing up to violent thugs from both the Left and the increasingly assertive Islamic communities in Britain, and they deserve the support of all free people."