Improving species delimitation and knowledge on species complexes is crucial for many areas of study in Biology, especially conservation. Integrative taxonomy contributes to this topic by using different approaches to better delineate taxonomic boundaries. Metternichia (Solanaceae), historically a monospecific genus, has a geographic range that comprises contrasting environments. Metternichia principis was described as having two varieties: the typical variety, found in the humid forests of eastern Brazil (Atlantic Forest region), and M. principis var. macrocalyx, which presents a larger calyx and inhabits mostly semi-arid areas (Caatinga region). In this study, we tested the validity of such groups by integrating environmental, phenological, morphometric, and palynological data; applying uni- and multivariate tests; and evaluating the conservation status of each taxon. Our results support the recognition of two morphological groups within Metternichia, largely in agreement with the original circumscription of the varieties. Multivariate analyses clearly indicate different ecological niches, with each taxon inhabiting environments with distinct mean annual precipitation and temperature. Phenological data show some differences between the varieties regarding months with the highest number of flowering and fruiting records. In general, M. principis var. macrocalyx presents larger flower and pollen characters, and smaller fruit characters compared to the typical variety. Based on these findings, we elevate the variety to the status of species, as the new combination Metternichia macrocalyx. Following IUCN guidelines, both taxa are here preliminarily considered endangered (EN).