Physicochemical, Bioactive, and Agroclimatic Differentiation of High-Andean Specialty Coffees Oriented toward Traceability and Territorial Valorization

High-Andean specialty coffees exhibit compositional properties associated with origin, variety, and agroclimatic growing conditions. The objective of this study was to differentiate green coffee varieties from the Cooperativa Agraria Cafetalera Valle de Incahuasi, Peru, through physicochemical properties, bioactive compounds, instrumental color, FTIR, multivariate analysis, and agroclimatic characterization using GIS tools. The varieties known as Geisha Blend, Geisha 90+, Caturra, and SL-09 were evaluated. The results showed significant differences among varieties (p < 0.05). Moisture ranged from 9.40 to 11.24%, protein from 11.08 to 12.89%, fat from 6.93 to 8.21%, carbohydrates from 64.58 to 67.39%, and crude fiber from 23.97 to 37.32%. Geisha 90+ showed the highest crude fiber, carbohydrate, total phenolic compound content (33.27 mg GAE/g db), and luminosity (L* = 51.71). In contrast, Caturra stood out for its higher protein, fat, ash, and caffeine content (9.36 mg/g db), as well as its chromatic values a* and b*. FTIR analysis revealed spectral profiles associated with lipid, caffeine, carbonyl, chlorogenic acid, alkaloid, polysaccharide, and trigonelline functional groups, reinforcing the chemical differentiation of the evaluated coffees. PCA explained 84.32% of the total variability, confirming a clear varietal separation. GIS information allowed the delimitation of ten study zones and the generation of maps of location, roads, hydrography, slopes, vegetation cover, and altitude. These results provide technical evidence to strengthen the traceability, authenticity, and territorial valorization of High-Andean specialty coffees.