Remaining habitat for P. tapanuliensis is threatened by forest fragmentation, habitat degradation, and conversion that are slated to continue. These are critical factors for the survival of large primates, and particularly Sumatran orangutans, including P. tapanuliensis. Presently, individuals of this species are divided among three forest fragments in the Batang Toru region of Sumatra.

The native forests of Borneo have been impacted by selective logging, fire, and conversion to plantations at unprecedented scales since industrial-scale extractive industries began in the early 1970s. There is no island-wide documentation of forest clearance or logging since the 1970s. This creates an information gap for conservation planning, especially with regard to selectively logged forests that maintain high conservation potential.