The rise of terrorism in Nigeria and the government's response by establishing various counter-terrorism legislations, policies and institutions to curb the trend has become a major source of concern to observers and scholars on the effects of these measures on human rights. However, there is a dearth of research on the implications of this policies on civil society organizations in Nigeria. This study therefore examines the various elements associated with or implicated in the interface between the counter terrorism security framework of the government and the capacity of civil society organizations to carry out their mandates in Nigeria. In order to achieve this, the survey research of the ex-post facto type will be adopted using the multi-stage sampling technique. All collected data will be coded and analysed using the Statistical Package for Social Science (SPSS). Content analysis will be used for the In-depth interview and secondary data.