Waste management has become pertinent in urban regions, along with rapid population growth. The current ways of managing waste, such as refuse collection and recycling, are failing to minimise waste in cities. With urban populations growing worldwide, there is the challenge of increased pressure to import food from rural areas. Urban agriculture not only presents an opportunity to explore other means of sustainable food production, but for managing organic waste in cities. However, this opportunity is not taken advantage of. Besides, there is a challenge of mixed reactions from urban planners and policymakers concerning the challenges and benefits presented by using organic waste in urban agriculture. The current paper explores the perceived challenges and opportunities for organic waste utilisation and management through urban agriculture in the Durban South Basin in eThekwini Municipality in KwaZulu-Natal (KZN) Province of South Africa. It is anticipated that this information will be of use to the eThekwini Municipality, policymakers, researchers, urban agriculture initiatives, households and relevant stakeholders in the study areas and similar contexts globally. Two hundred (200) households involved in any urban farming activity and ten (10) key informants (six (6) staff from the Cleaning and Solid Waste Unit of the eThekwini Municipality and four (4) from the urban agricultural initiative) were selected using convenient sampling. Descriptive statistics and inductive thematic analysis were used to analyse data. The significant perceived challenges and risks associated with the utilisation of organic waste through urban agriculture included lack of a supporting policy, climatic variation, lack of land tenure rights, soil contamination and food safety concerns. Qualitative data further showed that the difficulty in segregating waste, water scarcity, difficulty in accessing inputs, limited transportation of organic waste, inadequate handling and treatment of organic waste, and being a health hazard were some important challenges. On the other hand, the significant perceived benefits associated with the utilisation of organic waste through urban agriculture were enhanced food and nutrition security, and opportunities for business incubation. Other important benefits established through qualitative data were an improved market expansion for farmers and improved productivity. Overall, despite the perceived challenges and risks, there is an opportunity to manage organic waste through urban agriculture. It is imperative for an integrated policy encompassing the food, climate and waste management to be developed to support this strategy. All stakeholders—the government, municipal authorities and urban agricultural initiatives should also, guided by the policy, support urban farmers, for example, through pieces of training on how to properly manage and recycle organic waste, land distribution, inputs availability and water usage rights among other things.