The fruit bodies have dark brown caps that are up to 13 cm (5.1 in) in diameter and covered with patches of soft greyish-brown scales or warts.

The gills underneath the cap are crowded together, free from attachment to the stem, and white, becoming tinged with yellow in age.

Amanita nothofagi is a mycorrhizal species, and grows in association with native New Zealand trees such as Southern Beech.

[4] The cap of A. nothofagi is initially convex, later becoming flattened with a central depression, with radial grooves on the margin, reaching diameters of 3–13 centimetres (1–5 inches).

The remnants of the volva form small to large, irregularly shaped, felted patches, that are dull greyish-sepia to sepia, and sometimes scab-like.

Under a microscope, the spores appear hyaline (translucent), and are amyloid—meaning they will turn bluish-black to black when stained with Melzer's reagent.

A reliable method to distinguish the two is to check for the presence of clamp connections at the bases of the basidia, which are present in A. australis and absent from A. nothofagi.

A. luteofusca is also similar in appearance, spore size, amyloid reaction, and lack of clamp connections in the basidia.

It is distinguished from A. nothofagi largely on the basis of colour; it is a greyish-brown to yellowish-grey brown that fades to pinkish-buff as it gets older.