Altitude Modulates the Effect of Agricultural Management on Phenolic Compounds, Caffeine, and Cup Quality of Roasted Coffee (Coffea arabica L.) from Veracruz, Mexico

Coffee quality results from the interplay between genotype, environment, and cultivation practices, but whether the effect of agricultural management depends on altitude remains poorly understood. We hypothesized that the response of roasted coffee chemistry and cup quality to management would differ among altitudinal zones. Composite samples representative of sustainable and conventional management in three altitudinal zones (low, <900; mid, 900–1100; high, >1100 m.a.s.l.) were obtained from eighteen commercial Coffea arabica L. farms in Veracruz, Mexico (management monitored in 2023–2024 and 2024–2025; cherries sampled in the 2024–2025 harvest), and their physicochemical properties, phenolic compounds, caffeine, in vitro antioxidant capacity, and Specialty Coffee Association (SCA) cup quality were evaluated. Altitude was the main source of variation in pH, total phenolic and flavonoid contents, and total cup score. In contrast, management mainly affected chlorogenic acids (CGA), caffeine, and hydrolyzable tannins, which were higher under sustainable management (CGA: 22.52 vs. 16.82 mg g−1). The management × altitude interaction was significant (p ≤ 0.017) for all phenolic compounds, caffeine, and antioxidant assays, with the largest differences between systems in the mid zone, where sustainable samples showed the highest CGA (30.27 mg g−1) and FRAP values (675.30 µmol Trolox equivalents g−1). All samples reached specialty grade (82.08–84.75 points); total cup score increased with altitude and did not differ between management systems. These results indicate that management effects on coffee chemistry depend on altitude.