The attacks on the Twin Towers in New York in September 2001 and subsequent events not only ignited a 'war on terror', but also marked a crucial change in the policies on integration of migrants of Islamic background in Europe. Most countries departed from integration policies based on some sort of recognition of cultural diversity and emphasized national culture as the only legitimate format for citizenship. The result is a strengthening of a frame of governance with the aim to regulate Islamic practices and to mould outlooks, institutional settings and legal arrangements into the nation-state format. This has been referred to as the 'domestication of Islam'. One of the consequences is the narrowing down of research agendas and academic knowledge production. In this article I explore this process and address important fields of study that tend to be neglected in the study of Islam in Europe. © 2012 © 2012 Taylor & Francis.