Indonesia contributes significantly to deforestation in Southeast Asia. However, much uncertainty remains over the relative contributions of various forest-exploiting sectors to forest losses in the country. Here, we compare the magnitudes of forest and carbon loss, and forest and carbon stocks remaining within oil palm plantation, logging, fiber plantation (pulp and paper), and coal mining concessions in Indonesia. Forest loss in all industrial concessions, including logging concessions, relate to the conversion of forest to nonforest land cover. We found that the four industries accounted for ∼44.7% (∼6.6 Mha) of forest loss in Kalimantan, Sumatra, Papua, Sulawesi, and Moluccas between 2000 and 2010. Fiber plantation and logging concessions accounted for the largest forest loss (∼1.9 Mha and ∼1.8 Mha, respectively). Although the oil palm industry is often highlighted as a major driver of deforestation, it was ranked third in terms of deforestation (∼1 Mha), and second in terms of carbon dioxide emissions (∼1,300–2,350 Mt CO2). Crucially, ∼34.6% (∼26.8 Mha) of Indonesia's remaining forests is located within industrial concessions, the majority of which is found within logging concessions (∼18.8 Mha). Hence, future development plans within Indonesia's industrial sectors weigh heavily on the fate of Southeast Asia's remaining forests and carbon stocks.