The crust-like thallus of Malmidea lichens has a surface that varies from smooth to rough, featuring textures such as verrucose (wart-like), granulose (grainy), or pustulate (pimpled).

These textures are often formed by goniocysts, which are spherical clusters of green algal cells from the family Chlorococcaceae, encased in fungal hyphae.

These variously shaped surface bumps are often formed by goniocysts (spherical aggregations of photobiont cells surrounded by short-celled hyphae) that develop on a whitish fibrous underlying prothallus.

The hypothecium (the layer of hyphal tissue immediately beneath the hymenium) is prosoplectenchymatous (a cell arrangement where the hyphae are all oriented in one direction), and translucent to dark brown.

[3] Secondary chemicals associated with Malmidea include atranorin, sometimes norsolorinic acid (as in M. piperis), anthraquinones, biphenyls and many unknown xantholepinones.