High-quality Brazilian Canephora coffees are rising to the level of specialty coffees in the face of a new industry perception. In this framework, spectra from 527 coffees were analyzed in the near-infrared (NIR) region. Prin-cipal component analysis distinguished Brazilian Canephora producing states, botanical varieties, low and high -quality Canephora, Canephora and Arabica, and Canephora with geographical indication (GI) from those without GI. Also, Canephora coffee cultivars from Western Brazilian Amazon were distinguished. Three multi-class PLS-DA (traditional, hard, and soft versions) were compared to discriminate 5 classes: Robusta Amazonico from traditional (1) and indigenous (2) producers of Rondonia, Conilon from Espirito Santo (3), Conilon from Bahia (4), and specialty Arabica (5). Binary PLS-DA discriminated GI Canephora and non-GI Canephora with 100% sensitivity and specificity. Carbohydrates, chlorogenic acids, lipids, caffeine, and proteins were dominant ab-sorption bands in coffee classifications. The proposed method is objective, simple, fast, and could be used in the routine analysis of coffee to verify claims of identity, variety, and origin.