This research uses an organisational lens to explore the experiences and strategies of Pakistani transnational organisations based in London, Toronto and New York City. Using an original database of Pakistani migrant organizations, 131 in-depth interviews and over 200 hours of participant observation, I examine how the global war on terror results in the stigmatisation of Pakistani migrant transnational organisations that provide a range of social services in Pakistan. Findings reveal that Pakistani migrant organisations in all three cities encounter similar forms of organisational stigma. This stigma, in turn, makes is difficult for Pakistani migrant transnational organisations to fulfill their missions and meet the needs of communities in Pakistan. The paper offers new empirical and theoretical insights into the ways in which the regulatory environment associated with the war on terror constrains and prohibits Pakistani migrant organisations from delivering social services in Pakistan. Thus, this research shows how migrants’ efforts to contribute transnational social protection through organisations is hindered by racialised stigmatisation of Pakistani migrants and their organisational infrastructures.