Agathis kinabaluensis is currently only known from two locations. Although both are within protected areas, the relatively small size of their subpopulations and limited distributions make them susceptible to stochastic events. In addition there is some evidence of logging and forest clearance in the southern locality and from this a continuing decline is inferred. The small extent of occurrence (EOO=3,189 km²) and area of occupancy (AOO=92 km²) therefore place the species in the category Endangered. No additional information has been received since the last assessment (2013) so its conservation status remains unchanged.

The species is only known from Mt Kinabalu in Sabah and Mt Murud in Sarawak (Malaysia). The Flora Malesiana account (de Laubenfels 1988) identifies the Mt Murud subpopulation as Agathis orbicula.

There are two disjunct small subpopulations of this species between which there is no genetic exchange due to the distance. The Mt Kinabalu subpopulation is presumed to be stable while the trend of the Mt Marud subpopulation is likely to be declining due to logging and deforestation at least at the periphery of the subpopulation.

Agathis kinabaluensis is found in upper montane forest, mossy low forest and subalpine scrub (at altitudes between 1,500 and 2,400 m). It occurs on nutrient-poor substrates such as ultramafics, granite or sandstone.

The relatively small size of the two known subpopulations and their limited distribution make them vulnerable to stochastic events. In the areas surrounding Pulong Tau National Park Agathis spp. are used locally for house construction. Within the park, Agathis is used for building walkways for tourists (Pearce 2006). The extent to which these activities have effected A. kinabaluensis is uncertain.

This is a minor species occurring in remote mountain sites, if on ultramafic rock the trees are too small to be of interest for timber as there are other larger species of Agathis in the region. Some of the trees have been logged for local use.

The Mt Kinabalu subpopulation is almost entirely contained within the Mt Kinabalu National Park while the Mt Murud population is included within the recently declared Pulong Tau National Park. The species is in two ex situ collections (BGCI 2019).