This species grows terrestrially in a wide range of habitats, including upper montane mossy forest, secondary vegetation, ridge tops, cliff sides, and landslides. It has also been recorded at the margins of montane forest around the so-called Bonsai Forest, which is named for its stunted trees. The species is restricted to ultramafic substrates. While N. micramphora tolerates shady conditions, it grows best under direct sunlight. On Mount Hamiguitan, N. micramphora is sympatric with N. alata (sensu lato), N. justinae (previously identified as N. mindanaoensis), and N. peltata, and grows in the same altitudinal range as N. hamiguitanensis. Despite this, no natural hybrids have been observed with certainty.