This paper provides a critical viewpoint on the governance of Islam in Albania. Governance is understood as the relationship between state intervention and societal autonomy. The findings suggest that the governance of Islam in Albania is largely based on societal autonomy. The paper argues that this mode of governance, which has evolved since the end of the communist regime, has allowed the creation of opportunity structures for radicalisation and promotion of Islamist ideology. To illustrate this argument the paper analyses the legal and institutional framework for the relations between the Albanian state and the Albanian Muslim Community. This aim of this paper is to contribute to the debate on religion and security by making evident the logic of governance and to propose a research agenda that contributes to policy solutions through a theoretically guided approach.