Tourism’s environmental impact through increased waste generation poses risks to the tourism industry itself. Labuan Bajo, a rapidly developing tourism destination, needs an effective waste management system. A qualitative evaluation assessed technical operations, financing, institutions, regulations, and community roles. The results identified weaknesses in Labuan Bajo’s waste management system. Conventional collect-transport-dispose methods persist, and waste sources lack segregation, leading to mixed waste. Waste from liveaboard boats is collected at the port as a requirement for cruise permits. Waste fees are determined by source type, not waste volume. Only the local government’s environmental agency manages waste, while authority and regulations differ between provincial and district governments regarding waste in water and land. The community’s limited involvement includes insufficient participation in government-led initiatives like waste bank programs and socialization efforts. Given the interrelatedness of waste management aspects, improvements in one area necessitate support from others.