Coffee quality arises from the interaction among genotype, environment, and postharvest management, yet few large-scale studies jointly integrate agronomic, phytochemical, and processing traits. We characterized 150 Coffea arabica L. accessions from six Peruvian regions, evaluated in the INIA coffee germplasm collection, quantifying agro-morphological traits, colorimetric parameters in cherries and beans, fermentation indicators, bioactive compounds, and antioxidant activity. Correlation analyses showed that total phenolics (TPCs) and total flavonoids (TFCs) were strongly associated with antioxidant activity, whereas caffeine content (CAF) varied, largely independently. Several chromatic parameters in parchment and green coffee (a*, b*, C*) showed positive correlations with phenolic content and antioxidant activity (ABTS, DPPH, FRAP), while final fermentation pH (FPH) was negatively associated with these compounds, supporting both color metrics and pH as operational indicators of chemical quality. Principal component analysis disentangled a morphometric gradient from a functional (phenolic–antioxidant) gradient, indicating that bean size and antioxidant potential can be improved in a semi-independent manner. Hierarchical clustering identified complementary ideotypes, and a multi-trait selection index highlighted promising accessions—PER1002197 (Cajamarca), PER1002222 (Cajamarca), PER1002288 (Pasco), and PER1002184 (Cajamarca)—that combine high phenolic/antioxidant levels, favorable chlorogenic acid (CGA)/trigonelline (TGN) profiles, contrasting (high/low) caffeine, and competitive yield (YPP)/bean size. These accessions represent promising candidates for breeding climate-smart and nutraceutical-oriented coffee.

In recent years, Peruvian coffee production has increasingly focused on specialty coffees, with cup quality (CQ) as a key criterion. While previous studies have characterized the Coffee Germplasm Collection of the National Institute of Agrarian Innovation (CGC‐INIA), few studies have analyzed coffee cup quality. The present study assessed the association between agro‐morphological traits and sensory quality of CGC‐INIA. A total of 123 accessions from six departments were evaluated during two crop seasons (2022–2023 and 2023–2024). Fourteen agro‐morphological traits (morphological, reproductive, and phytosanitary) and cup quality were recorded. Mean cup quality of the accessions was 81.56 points, which is classified as “very good” according to the Specialty Coffee Association. Most traits remained stable across seasons, except for fruit production and two phytosanitary traits (leaf miner infestation and rust incidence). Correlation analysis showed weak associations between individual agro‐morphological traits and CQ ( r < 0.3). Principal component analysis explained 28.6% of the total variance in the first two components, indicating limited overall association between agro‐morphological variation and sensory quality. Generalized linear model results showed that Plant height (PH) and young shoot color (YSC) were the only traits positively associated with CQ. However, the weak associations and small effect sizes indicate that PH and YSC should be considered complementary indicators in CQ evaluation, and only within integrated selection frameworks that combine phenotypic, genetic, environmental, and management factors to improve specialty coffee quality.

Mineral composition modulates plant health, agro-morphological attributes, and functional quality in coffee, yet large-scale evaluations remain limited. In 150 Coffea arabica L. accessions, we quantified grain minerals (Ca, K, Mg, Na, P, Zn, Cu, Fe, Mn); resistance to coffee leaf miner (CLM), coffee berry borer (CBB), and coffee leaf rust (CLR); agro-morphological traits; bioactive compounds (phenolics, flavonoids, chlorogenic acid, trigonelline, caffeine); and antioxidant capacity (ABTS, DPPH, FRAP). Mn and Zn were associated with greater resistance to CBB and CLM, whereas P and Ca related with lower susceptibility to CLR; a P–Zn antagonism emerged as a critical nutritional axis. Phosphorus was linked to larger size and higher 100-bean mass; Ca and Mg to greater fruit number and fruit mass per plant; and Fe to improved filling and higher 100-bean mass in parchment coffee. For bioactive compounds, P and K were positively associated with total phenolics, total flavonoids, caffeine, and ABTS/FRAP antioxidant activity, while trigonelline and chlorogenic acid correlated positively with the micronutrients Zn, Cu, and Fe. Cluster analysis resolved groups associated with resistance, Zn/Fe biofortification, productivity, and functional quality. PER1002287, PER1002216, PER1002207, and PER1002197 emerged as promising accessions balancing plant health, yield, and phytochemical quality. Overall, grain mineral composition is linked to plant health, productivity, and functional quality in coffee, providing a foundation for precision nutrient management and breeding programs aimed at resilient and high–value-added coffee.