In the chase to reduce global warming and climate change, researches have focused on finding better ways to reduce pollution and harmful emissions. One way to reduce those emissions is the use of bio-fuel as an alternative source of fuel. Until recently, with bio-fuel being used increasingly in the market, new problems have started to emerge. One of the problems is the use of food-crops and homogeneous crops in farmlands which in turn increases food prices and reduce available lands for other crop types. Beside pricing and sustainability issues, most research is often in nation with good infrastructure or with established markets. Although, there is clear evidence that in the future, Emerging Markets (EM) nations would become the biggest consumers of bio-fuel. Nations such as Indonesia, which is noted by McKinsey as a future major user of bio-fuel, could also contribute in high amounts of bio-fuel production for the ASEAN region. Combined with the high amount of agricultural production, there is bound to be more than enough biomass in the region to sustain bio-refineries in Indonesia. The problem of producing bio-fuel in Indonesia is not only about infrastructure, but also the use of sea-vessel to transport biomass to bio-refineries. To create a sustainable and green logistics, it is of the utmost importance that generating and shipping of bio-fuel have less carbon emissions then the proposed offset from the usage of bio-fuel. Therefore, an efficient logistic is the key factor in achieving the goal. This study will also consider sea-vessel transportation to and from bio-refineries across the Indonesian archipelago.