This species was diagnosed by Andersson (1998) as having thicker-textured elliptic leaves that are shiny above and have tufted domatia, the calyx limb 2.5-5 mm long with well developed narrow lobes, medium-sized flowers with the corolla tube 9-13 mm long, and stout, ellipsoid, thicker-textured capsules. These fruits resemble those of many species of Ladenbergia.
Andersson compared Cinchona macrocalyx to several others with similarly thick stout fruits. He distinguished C. pitayensis by its broader leaves and corolla tube that is glabrous or only sparsely pubescent inside; C. krauseana by its larger flowers, with the corolla tube 12-20 mm long; and C. hirsuta and C. officinalis by their leaves with pit domatia.