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The main goal of this work was to investigate the relationship between the fruit morphology and biochemical composition of peppers (<i>Capsicum</i> spp.). For that purpose, one hundred native varieties from the Andean region, where the genus <i>Capsicum</i> has its origin, were analysed for different phytochemical compounds. In addition, pepper fruits were assessed with the highly precise phenomics tool Tomato Analyzer. The collection showed a broad variability which was more evident within the <i>C. annuum</i> group. On average, <i>C. frutescens</i> accessions displayed the highest levels of solid soluble content, pH, polyphenols and antioxidant activity. The Tomato Analyzer descriptors under the categories of size, shape index, and latitudinal section, mostly contributed to the variance among <i>Capsicum</i> groups. <i>C. annuum</i> hold the larger fruits, whereas <i>C. frutescens</i> comprised fruits of smaller sizes. The correlation analysis revealed that biochemical traits were negatively correlated with the fruit parameters related to size, suggesting that huger fruits contain lower amounts of chemical metabolites. The multivariate approximations demonstrated that Andean peppers assorted according to morphometric and colorimetric characteristics, but independently of their species or geographical origin. Groups of valuable native varieties carrying promising traits were identified.