Throughout the last decades, integration programmes in Western Europe have centrally revolved around debates on Muslim populations and the institutionalization of Islam. The concept of integration has become a master paradigm with which to structure plurality of immigration societies across Western Europe. Critically reflecting this inflation, this article argues that the integration of Muslims is animated by a contingent liberal-secular matrix through which the sovereign state, in close connection with civil society, is enabled to decide what counts as proper and improper religion. Integration directed toward Muslims as a “religious minority” is therefore indicative of the very problems that it purports to resolve. In a genealogical vein, the article begins by suggesting that integration is a liberal “recursion” of earlier projects of minority management such as assimilation and conditional recognition within emerging nation-states. It argues that the epistemological ground which animated the assimilatory forces of the modern nation-state has been intimately bound by an imperial knowledge order which classifies and hierarchizes people along a race-religion nexus. The analysis continues by dwelling on contemporary examples of state organized dialog with Muslims, and more specifically the establishment of Islamic Theology Chairs at state universities. Through these examples the article shows that the institutionalization of Islam in Europe reconfigures a pattern which conditionally embraces religious difference, while at the same time continuing hierarchical rankings and by transforming it to make it fit for religion's legitimate place in public life. Finally, the article suggests that the somatic aspirations prevalent in assimilation projects and imperial race-religion constellations are both inscribed and concealed in the frequent invocation of Muslims to reveal their loyalty to the liberal-secular contract by bracketing their religious sensibilities for the sake of secular reason.