High-quality canephora coffees (Robusta and Conilon botanical groups) from Brazil are attracting increasing attention for their unique and distinctive sensory characteristics. This study proposed a near-infrared spectroscopy and chemometric discrimination and classification of Brazilian canephora coffees with certified geographical indication, uncertified canephora, and specialty Arabica coffees using near-infrared technology as a spectral fingerprint to capture the identity of each coffee. Five hundred and twenty-seven roasted and ground coffee samples from Brazil were analyzed in this study and five classes were discriminated: Robusta Amazônico produced in Rondônia by indigenous producers (1) and traditional coffee producers (2) in the Brazilian Amazon Rainforest region with Designation of Origin (DO) “Matas de Rondônia”, Conilon from Espírito Santo (3) with Indication of Origin (IO) “Espírito Santo”, Conilon from Bahia (4) without certification, and specialty Arabica coffees of different origins and sensory profiles (5). Conilon from São Paulo and low-quality canephora coffees were also analyzed for comparison purposes. At the first glance, there was a slight distinction between Robusta Amazônico and Conilon from Espírito Santo compared to Arabica, Conilon from Bahia and low-quality canephora coffees spectral fingerprints. This result is consistent because Rondônia and Espírito Santo have been contributing to the production of quality canephora coffee and this makes these coffees distinctive. A multi-class partial least squares discriminant analysis (PLS-DA) allowed to correctly discriminate and classify the five groups according to geographic origin and general characteristics with sensibility and specificity greater than 90% in external validation. Finally, a chemical interpretation of the most discriminant variables was performed using the variable importance in projections scores. This study is a pioneer in coffee science field and recent developments in canephora quality. It will be important for assessing the biodiversity and geographical identities of Brazilian Conilon and Robusta with a routine method in coffee origin inspection and certification agencies.