This species is characterized by its shrub habit, small petiolate elliptic leaves with the secondary veins impressed on the upper surface, short spiciform inflorescences with the subsessile flowers borne singly along the primary axis, deeply lobed calyx limbs with lanceolate to narrowly triangular lobes, white to pink corollas with funnelform tubes ca. 4 mm long and rounded lobes ca. 2 mm long, and 4-locular fruits that firsr become bright red then turn white when mature. The leaves are smooth on the lower surface, with the secondary veins prominent and densely strigillose but the remaining area smooth and sparsely strigillose to glabrescent. The inflorescences are initially short and cymose with 3-5 buds, then as flowering proceeds the primary axis elongates, up to 15 cm long with ca. 25 flowers. A rand of inflorescence form is seen in the set of collections from Cerro de Torrá, an isolated montane site, from shortly cymose (Silverstone-Sopkin et al. 1524) to spiciform with a well developed axis ca. 3 cm long (Silverstone-Sopkin et al. 4141).

Two varieties of Gonzalagunia discolor have been named, with var. danielis having smaller leaves and found in Antioquia, Colombia. The characters of the species listed above are for var. discolor.

Gonzalagunia discolor is similar to Gonzalagunia sororia, with usually larger leaves that have the tertiary venation regularly well developed and raised on the lower surface. Gonzalagunia discolor is also similar to Gonzalagunia pauciflora of Ecuador, which has pedicillate flowers and shallowly divided calyx limbs with deltate obtuse lobes; this other species was also distinguished originally by its shorter inflorescences, but its inflorescences are in fact similar some plants with quite short axes in Gonzalagunia discolor.