This article problematises protection for lesbian, gay, bisexual, transgender, and intersex (LGBTI) refugees in contexts of state-condoned persecution against this group. Based on ethnographic evidence from Kampala, Uganda, we draw attention to the homogenising tendencies of centralised protection systems in cities in the global south, which are primarily centred on nationality-based communities. We examine the processes of social exclusion that limit the involvement of LGBTI refugees from the Great Lakes Region in such communities, de facto placing them outside the parameters of institutional refugee protection. We then focus on their relational experiences of protection and safety within the office of an LGBTI support group in Kampala and argue for a micro-level approach that considers how LGBTI refugee protection is grounded in the geopolitics of the everyday. Our findings underscore the limitations of institutional policy and practice, which continues to overlook the protection gap that exists for LGBTI persons within the refugee population in Uganda. In order to remedy this protection gap, we suggest that a critical reconsideration is needed of the participatory spaces and cooperation between LGBTI refugee-led advocates and refugee serving institutions and decision-makers.