Combining protected areas with natural forest timber concessions may sustain larger forest landscapes than is possible via protected areas alone. However, the role of timber concessions in maintaining natural forest remains poorly characterized. An estimated 57% (303,525 km²) of Kalimantan's land area (532,100 km²) was covered by natural forest in 2000. About 14,212 km² (4.7%) had been cleared by 2010. Forests in oil palm concessions had been reduced by 5,600 km² (14.1%), while the figures for timber concessions are 1,336 km² (1.5%), and for protected forests are 1,122 km² (1.2%). These deforestation rates explain little about the relative performance of the different land use categories under equivalent conversion risks due to the confounding effects of location. An estimated 25% of lands allocated for timber harvesting in 2000 had their status changed to industrial plantation concessions in 2010. Based on a sample of 3,391 forest plots (1×1 km; 100 ha), and matching statistical analyses, 2000-2010 deforestation was on average 17.6 ha lower (95% C.I.: -22.3 ha- -12.9 ha) in timber concession plots than in oil palm concession plots. When location effects were accounted for, deforestation rates in timber concessions and protected areas were not significantly different (Mean difference: 0.35 ha; 95% C.I.: -0.002 ha-0.7 ha). Natural forest timber concessions in Kalimantan had similar ability as protected areas to maintain forest cover during 2000-2010, provided the former were not reclassified to industrial plantation concessions. Our study indicates the desirability of the Government of Indonesia designating its natural forest timber concessions as protected areas under the IUCN Protected Area Category VI to protect them from reclassification.