The rapid urbanization in major cities, e.g., Phnom Penh, Cambodia, increases the concern for the integrated waste management of municipal solid waste and sewage as a social responsibility toward the public welfare. While high-income countries are gearing toward integrating waste management into the circular economy, low-to-middle income countries are still facing various challenges ranging from infrastructure investment to societal acceptance. Despite all barriers, mining the potential opportunity from the circular economy framework in waste management in terms of nutrient recycling from bio-wastes such as food waste and human excreta is yet to be explored; the difficulty and complexity in co-managing the urban bio-wastes anchor in switching from linear to circular thinking. This study aims to understand the barriers to implementing such co-management of organic waste and human excreta in Phnom Penh, the capital city of Cambodia, using the Decision Making Trial and Evaluation Laboratory (DEMATEL) methodology. The results show that the lack of regulatory enforcement and implementation to control the illegal disposal of municipal solid waste and septage waste is the key cause barrier. The highly linked barrier is the lack of appropriate collection, storage, and treatment system for municipal solid waste and septage waste. Thus, this study could provide insights into developing actionable policy recommendations to solve the issue of waste management while achieving SDG goals and exploring the benefit of a circular economy in Cambodia.