Tapioca starch and palm oil industries are considered as ones of the fast-growing agro-industries in Thailand. Both industries release a significant amount of wastewater with high organic content as a result of their production processes. Traditionally, open pond systems have been used to treat wastewater and consequently achieve compliance with environmental standards. Over the last few years however, more sustainable, expensive and modern alternatives have begun to be used to treat wastewater (mainly anaerobic reactors). The start of clean development mechanism (CDM) projects in Thailand has also contributed significantly to this expansion.1 One significant advantage of the anaerobic reactors, over the open ponds, is the possibility of capturing, in a controlled environment, the greenhouse gases (GHGs) generated, principally biogas with a high concentration of methane. The biogas can be used to generate heat and/or produce electricity, substituting fossil fuels as an energy source. The number of biogas utilization projects in Thailand and the Southeast Asia region has been increasing substantially in recent years. While a biogas plant can bring economic benefits with respect to energy self-sufficiency and cost-saving over time, the design and operation of a biogas plant requires high investments and is still perceived as a risky business due to a number of barriers. In addition, actual data from biogas plants indicate that the performance of a biogas plant with respect to the amount of biogas is not as attractive as it was initially expected among the project developers. Even though many literatures show the performance of biogas plants in certain experimental conditions, surprisingly, few literatures have explained or have shown data about the low performance of the biogas plants compared to the expected projected performance or design. The purpose of this study is to identify these barriers in biogas technology implementation and operation in Thailand, and to determine how these barriers lower the performance of the biogas business. The study was conducted based on the analysis of 48 selected CDM projects in Thailand and further analysis through consultation with relevant professionals in CDM and the biogas business in Thailand. The results of this study provide important lessons for future biogas utilization and greenhouse gas emission reductions in the Southeast Asian region.