This article examines the role of faith-based organizations (FBOs) in counter-radicalization in Nigeria, with emphasis on the Boko Haram terrorist group operating in northeast Nigeria and the greater Lake Chad region. A qualitative methodological approach is employed that makes use of primary and secondary documents, key informant and stakeholder interviews, and focus group discussions with critical religious actors and organizations. The findings of the article suggest that FBOs play a critical role in the disengagement and deradicalization process of countering the ideological and radical messages of Boko Haram. However, challenges such as the lack of effective stakeholder involvement in the various initiatives by the state in counterterrorism, fear of reprisal and attacks, lack of unison by various FBOs and clerics in countering these negative messages, and the inability of relevant stakeholders in addressing structural factors such as poverty, social and economic exclusion, and unemployment that give rise to radicalization amongst other challenges, have impeded the effectiveness of the FBO sector in its counter-radicalization efforts in Nigeria. To address these challenges, the article proposes a bottom-up approach to counterterrorism that provides room for the multi-sectoral involvement of major stakeholders, especially FBOs, to complement pre-existing initiatives and other measures to counter the negative weaponization of religion by radical and rogue clerics, and also to prevent Boko Haram from expanding its frontiers.