Bhekisisa was launched in January 2013 with financial support from the German government's Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ). The grant was a 50-50 private-public-partnership between the Mail & Guardian and GIZ and ended in June 2014. Bhekisisa then received another grant from GIZ, which ended in December 2014.  

In September 2015 Bhekisisa received financial support from the Bill and Melinda Gates Foundation to expand its activities to Africa. The funding covers most of the Bhekisisa staff's salaries, their travel to African countries and the cost of freelance in-country correspondents.