South Africa has a progressive legal refugee framework and retains a national refugee reception system comprising of several key pieces of institutional architecture, which include a nationally run refugee status determination (RSD) procedure, and appeal and judicial review mechanisms. All of these are prescribed in law to ensure implementation of the state’s international obligations towards asylum-seekers and refugees. Yet, since being established in the mid-1990s, the national refugee reception system, which is overseen by the Department of Home Affairs (DHA), has been plagued by allegations of corruption, serious legal and procedural flaws in the application of the law, and national policies that continually breach international law. This article asks what impact the overarching management of refugee affairs being under the control of DHA has had on individual institutions. Has the DHA been able to truly assert influence over all aspects of the asylum system or have individual institutions been able to carve out their own institutional identity which helps insulate them from broader ideology and allows them to place their mandate for the protection of refugees as a priority? In this way, the article speaks directly to the role institutional identity plays within national refugee reception systems and the impact these issues have on how government officials and institutions implement relevant legal frameworks. Ultimately, what emerges is a government department that from day one has been able to exert its influence over all aspects of refugee affairs, either through key pieces of institutional architecture, or by responding to perceived setbacks through new policy. The result is a national system that creates barriers that prevent asylum-seekers and refugees from gaining access to the interior and leaves most forced migrants in the country struggling to access basic rights. Equally, the mounting importance of the judiciary and civil society as the only de jure and de facto custodians of refugee protection in the country becomes explicit. The paper concludes by suggesting international agencies such as the United Nations High Commissioner for Refugees (UNHCR) should utilise recent developments through the Global Compact on Refugees as an opportunity to build stronger relations with the more progressive elements of the DHA and push for the reengagement and better co-operation with key stakeholders, such as civil society and academia.