Since the deployment of AMISOM, the EU has been one of the main funders of the operation, both through the African Peace Facility (APF), which is the EU's main instrument to support Peace and Security in Africa, and through bilateral contributions of its Member States.
Pärast AMISOMi käivitamist on EL olnud operatsiooni peamisi rahastajaid, kasutades selleks nii Aafrika rahutagamisrahastut, mis on ELi peamine vahend Aafrika rahu ja julgeoleku toetamiseks, kui ka liikmesriikide kahepoolset toetust.