Background: Metabolomic studies in Coffea spp. have identified agronomically important metabolites in leaves. However, endosperm metabolomics has focused on cup quality using processed beans, where chemistry composition is altered during fermentation. Therefore, these studies provide limited insight into defense metabolites present in planta. Hypotheses: Coffea spp. endosperms from different cultivars grown under similar conditions exhibit distinct chemical profiles according to its genotype, including differentially accumulated metabolites with potential biological activity against pathogens and pests. Studied species: Four Coffea arabica genotypes (Red Bourbon, Gesha, Pink Bourbon, and SL28) and four Coffea arabica introgressed with Coffea canephora (Mundo Maya, Marsellesa, Costa Rica 95, and Yellow Catucaí). Study site and dates: Demonstrative coffee plantation of Francisco Javier Clavijero Botanical Garden (the Instituto de Ecología A.C.), Xalapa, Veracruz and private conservation area Finca Metlapili, Coatepec, Veracruz on March 14-15, 2025. Methods: Freeze-dried matured endosperms were extracted with methanol via Accelerated Solvent Extraction. Extracts were analyzed by Ultra High-Performance Liquid Chromatography coupled to a High-Resolution Quadrupole Time of Flight mass spectrometer. Compounds were annotated using Progenesis QI and manually curated. Statistical and functional analyses were conducted in MetaboAnalyst. Results: Each genotype showed a characteristic chemical profile, grouping into Timor-related and Typica/Bourbon-related clusters. Sixty-nine compounds were identified, including polyphenols, alkaloids, terpenoids, lipids, amino acids, and organic acids. Most metabolites were differentially accumulated among genotypes, and several have documented biological activity or roles in plant defense. Conclusions: All Coffea spp. genotypes were distinguishable by their endosperm chemical profile. Several over-accumulated metabolites have reported roles in defense.