This article examines the EU’s promotion of the religious identity of Muslims within the context of European counter-terrorism measures. Counter-terrorism laws of the EU and its Member States impact on the religious identity of Muslims. They have an arguably disproportionate effect on the civil rights of individuals in the quest to combat terrorism and can be seen to increase Islamophobia in two ways: a rise in general discrimination against Muslims and a requirement on Muslims to distance their connection to Islamic practice and traditions. EU law dealing with terrorist offences speak little of this backlash that Muslims face in European countries. Although the EU has somewhat of a framework in place which concerns the protection of Islamic identity, the reluctance of the EU to take a determined stance on the issue of the protection of religious identity is illustrated through the ambiguous nature of its legislation.