In recognition of concerns about the security of energy supply and climate change, the Thai government has developed Alternative Energy Development Plan for the period 2012–2021. Under this plan, the production of bio- ethanol and biodiesel in 2021 is expected to grow significantly. This growth will add more pressures on water and land requirements for growing energy crops. This is likely to contribute to worsening the security of water and food supply. This paper, therefore, provides an overview of the bioenergy development and current policies in Thailand with a view to identify the challenges faced by the development of bioenergy. A review of the bioenergy policies reveals that the existing policies have been exclusively focus on energy perspective and largely ignore the significance of the implications arising from the interdependencies between energy, water and food. There is a lack of understanding of the interrelationships between bioenergy, water and food policy interactions. The lack of such understanding is likely to pose several challenges including food or fuel dilemma, security of water supply and issues surrounding land use for biofuel production. This paper further emphasizes the need to develop an integrated framework for developing an understanding of the relationships between energy, water and land.