This species is characterized by its shrub habit, strigose stems and inflorescences, ovate shortly petiolate leaves that are densely white-lanose on the lower surface, flowers arranged in small groups that are subsessile or borne on very short secondary axes, white small corollas with tubes 4-4.5 mm long, and white fruits with 4 locules. The white undersides of the leaves are distinctive, and separate it from other lowland South American Gonzalagunia species.

Gonzalagunia dependens also has densely white-lanose leaf undersides, but difers in its densely lanose or tomentose stems and inflorescences and is generally found at higher elevations, 1500-2000 m. However the ovary portions of the flowers of Gonzalagunia killipii are densely white-lanose, and the pubescence of the stems and inflorescence axes of Gonzalagunia dependens is often deciduous with age so specimens of these two species from premontane and montane vegetation with older stems or immature fruits can sometimes be subtle to differentiate.