"Nepenthes eustachya" differs from "N. alata" in a number of morphological features. Jebb and Cheek outlined these differences when they restored the former as a valid species. "Nepenthes eustachya" has a lamina with a rounded to sub- apex, whereas that of "N. alata" is lanceolate-ovate with an acute or apex. The petiole also serves to distinguish these species: in "N. eustachya" it is scarcely or not winged at all, whereas in "N. alata" it is broadly winged. The pitchers of "N. eustachya" bear a simple or spur, compared to the simple and acutely pointed appendage of "N. alata". Mature parts of "N. eustachya" are , while "N. alata" bears an indumentum of reddish or whitish hairs. Jebb and Cheek also compared the structure of the pitcher base: that of "N. eustachya" is angular and woody, being gradually attenuate towards the tendril. The base of "N. alata" traps, however, has a similar texture to the rest of the pitcher and is abruptly attenuate towards the tendril.