Efficient selection of potato varieties with enhanced nutritional quality requires simple, accurate and cost effective assays to obtain tuber chemical composition information. In this study, 75 Andean native potato samples from 7 Solanum species with different colors were characterized and quantified for their anthocyanin, phenolics and sugar content using traditional reference methods. IR (infrared) spectra of potato extracts were collected using a portable infrared system and partial least squares regression (PLSR) calibration models were developed. These models were validated using both full cross-validation and an independent sample set giving strong linear correlation coefficients of prediction (rPred) > 0.91 and standard error of prediction (SEP) of 24 mg/100 g phenolics, 7 mg/100 g monomeric anthocyanins, 0.1 g/100 g reducing sugars and 0.12 g/100 g sucrose. Overall, portable infrared system with PLSR showed great potential to facilitate potato breeding and certain aspects of crop management, material selection for potato processing and related research by providing alternative prediction models.