Microhyla nepenthicola is a very small forest-floor species associated with pitcher plants. We found it to be particularly abundant in forest-edge habitats. The maximum snout–vent length in females is 16 mm, but most specimens—particularly males—are smaller, ranging from 10.6 to 12.8 mm, making this the smallest known frog in Southeast Asia.

The frogs are brown above, in varying shades, some individuals tend to a greyish spectrum. The innermost (first) finger is highly reduced and indistinct in males, though it is more distinct in females. The other three fingers are well developed. Both finger and toe tips are expanded.

This tiny species is locally abundant where pitcher plants occur. Breeding groups are active both during the day (especially in the afternoon) and at night, in patches of pitcher plant growth—particularly in association with Nepenthes ampullaria.

The tadpoles of this species are very small and moderately pigmented. The tail terminates in a short flagellum. Tadpoles develop inside pitcher plant pitchers and are endotrophic, living off yolk reserves stored in their guts. They lack keratinized mouthparts. The mouth is terminal and slightly upward-facing. The spiraculum is located medially on the venter. When undisturbed, tadpoles remain mostly stationary in an oblique orientation, maneuvering by beating their tail tips.

The eyes of the tadpole are positioned far laterally on the head (a feature of micrcohylid tadpoles in general).

This species was described in 2010 from Gunung Serapi, within the Matang Range, western Sarawak. It is presumably widespread in suitable habitats throughout the lowlands of northwestern Borneo. As in many other species from Borneo, existing sampling data does not allow to establish a distribution map.