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This article explores how Muslim-led civil society organizations (CSOs) implement programs to Counter Violent Extremism (CVE) in Malindi, Kenya, while adapting these programs to both their local context and the CVE-policies of Western donors. So far, little research has been done on how East-African Muslims relate themselves to (global) anxieties about Islam and violent extremism. Taking theories within the anthropology of secularism as an analytical frame, I argue that although Western donors try to maintain a public stance of neutrality towards different religions, they perpetuate stigmatizing associations between Islam and terrorism by tacitly mobilizing a distinction between ‘moderate’ and ‘radical’ Muslims. Based on extensive ethnographic research, I subsequently analyze how Muslim-led CSOs strategically navigate and challenge these stigmatizing associations as they implement CVE programs in Malindi. I also show how the desire to present Islam as peaceful limits possibilities to address widespread feelings of marginalization among Kenyan Muslims.