In Africa, the linkages between zoning planning and affordable housing have not been adequately assessed. In scenarios where zoning system has been enforced for a long time, such as in the United States, it has been often labelled as exclusionary due to how it limits the poor to access housing. With zoning being at the heart of the current planning system in Rwanda, this research aims at examining these linkages in an emerging urban setting such as Kigali city. This study employed a mixed-method approach to assess how the master plan and zoning requirements affect housing cost and the ease of accessing housing for low-income households. Results reveal a total house supply gap to 30,000 units between 2012-2020 of which more than half is affordable housing. While zoning code requires the use of primarily imported materials which increases the cost of housing, more than 70 per cent of residents earn too minimal income to qualify for traditional mortgage loans. Therefore, the case of Kigali city emphasizes the mismatch between zoning assumptions and underlying social and economic conditions. Moreover, the euphoria to meet master plan objectives encourages the conversion of prevalent informal settlements into high-end market neighborhoods overlooking the negative impact on affordable housing. This study suggests the relaxation of zoning regulations for certain income thresholds, re-defining affordability to match the local context and generating housing affordability indexes regularly to inform the government’s urban housing strategies.