This policy brief highlights the role that donor headquarters play in shaping the incentives and rules of the aid system, influencing implementing partner decisions, policies, and investments. It takes a deeper look at how some well-meaning policies can unexpectedly backfire, leading to new challenges, inefficiencies or in some cases, perpetuate conflict. To do so, it analyses five well-meaning policies common to many donors that can have unexpectedly negative results within conflict-affected countries, providing examples from South Sudan. Lastly, the brief provides recommendations and guidance on how improvements can be made to tackle each policy’s potential negative effects.