**4. Conclusions**

This study reviewed the operational research methods used in biofuel supply chain planning. For the upstream supply chain optimisation, most optimisation focuses on either economic performance or environmental and social factors. For the downstream bioenergy trading optimisation, price and demand uncertainties are of the significant challenges for regional and international trading, which can be influenced by the policy or industry target of all trading partners involved. Following the increment in the mandate biofuel blend imposed by the three mentioned countries—Malaysia, Indonesia and Thailand—and the global demand for cleaner biofuel, the integration of the environmental and social factors to the supply chain design would offer better decision making on optimising the sustainability. The sustainability of bioenergy upstream supply chain can come to the negative environmental impact of bioenergy feedstock plantation due to land-use change, fertilisation and irrigation. Stricter qualification of advanced and greener biofuel for international downstream trading through the development of sustainability criteria and certification is crucial, especially the trade-offs of environmental and social footprints.

There is a consideration of the industry or policy's characteristic, such as a biofuel industry based on single biomass, the flexibility of other conversion technologies and the utilisation routes of the interested biomass. A more holistic approach that took sustainability criteria like land-use change, biodiversity loss, the impact of irrigation and fertilisation, carbon emission footprint, nitrogen footprint and other emission footprints into consideration is vital to assist a more informed policy decision. Good governance and coordination of different policy areas: an integrated assessment should support energy, land-use change, climate and rural socio-economic development. There is an urgent need for interdisciplinary research in this field, especially for the Southeast Asian countries which have a high forecasted annual biofuel production growth rate in years to come. While biofuel enables countries to meet their energy goals, established interdisciplinary research done in this field will lead to more sustainable resource use, improved environmental performance, strengthened energy security and enhanced economic development.

**Author Contributions:** Conceptualization, H.P.Y. and F.Y.V.; methodology, H.P.Y. and F.Y.V.; formal analysis, H.P.Y., C.B.P.C. and F.Y.V.; resources, H.P.Y., C.B.P.C. and F.Y.V.; writing—original draft preparation, H.P.Y., C.B.P.C. and F.Y.V.; writing—review and editing, H.P.Y., C.B.P.C. and F.Y.V.; visualization, H.P.Y. and F.Y.V.; supervision, H.P.Y. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by the Energy Studies Institute and the EU project "Sustainable Process Integration Laboratory—SPIL", project No. CZ.02.1.01/0.0/0.0/15\_003/0000456 by EU "CZ Operational Programme Research, Development and Education".

**Acknowledgments:** Energy Studies Institute is acknowledged for core funding this piece of work. The EU project Sustainable Process Integration Laboratory—SPIL, funded as project No. CZ.02.1.01/0.0/0.0/15 003/0000456, by Czech Republic Operational Programme Research and Development, Education under the collaboration agreement with the Universiti Teknologi Malaysia is gratefully acknowledged.

**Conflicts of Interest:** The authors declare no conflict of interest.
