Human activities generate waste and the amounts tend to increase as the demand for quality of life increases. Today’s rate in the Southeast Asian Nations (ASEANs) is alarming, posing a challenge to governments regarding environmental pollution in the recent years. The expectation is that eventually waste treatment and waste prevention approaches will develop towards sustainable waste management solutions. This expectation is for instance reflected in the term ‘zero emission systems’. The concept of zero emissions can be applied successfully with today’s technical possibilities in the agro-based processing industry. First, the state-of-the-art of waste management in Southeast Asian countries will be outlined in this paper, followed by waste generation rates, sources, and composition, as well as future trends of waste. Further on, solutions for solid waste management will be reviewed in the discussions of sustainable waste management. The paper emphasizes the concept of waste prevention through utilization of all wastes as process inputs, leading to the possibility of creating an ecosystem in a loop of materials. Also, a case study, focusing on the citrus processing industry, is displayed to illustrate the application of the aggregated material input–output model in a widespread processing industry in ASEAN. The model can be shown as a closed cluster, which permits an identification of opportunities for reducing environmental impacts at the process level in the food processing industry. Throughout the discussion in this paper, the utilization of renewable energy and economic aspects are considered to adapt to environmental and economic issues and the aim of eco-efficiency. Additionally, the opportunities and constraints of waste management will be discussed.