Biorefineries provide opportunities to improve the economic, environmental, and social performance of bio-based production systems. Prudent planning of plant configuration and localization is however of great merit to obtain maximum benefits from biorefineries. This study investigates optimal deployment of palm oil-based biorefineries on the two major islands of Indonesia, Sumatra and Kalimantan. In addition, the results of the optimal bioenergy (bioelectricity, biodiesel, ethanol) production are used to calculate the potential contribution of the palm oil industry according to the national bioenergy targets from 2020 to 2030. This work also offers a new perspective of analyzing the role of bioenergy in the palm oil industry in relation to meeting the bioenergy targets through the development of spatially explicit optimization model, BeWhere Indonesia. Results show that the palm oil-based biorefineries in Sumatra and Kalimantan can produce 1–1.25 GW of electricity, 4.6–12.5 bL of biodiesel, and 2.8–4.8 bL of ethanol in 2030. Significant efforts in terms of mobilization of resources and economic instruments are required to harness the full potential offered by the palm oil-based biorefineries. This study provides an important insight on how palm oil biorefineries can be developed for their enhanced roles in meeting global sustainability efforts.