Coffee processing involves various steps, from harvest to the storage of dried green coffee beans, each of which can significantly affect the beans' chemical composition and sensory qualities. Yet, a comprehensive evaluation that includes the coffee's genetic background and chemical, sensory, and biological aspects is still uncommon for Robusta coffee. Four Robusta (C. canephora) genotypes from the Democratic Republic of the Congo were subjected to five different coffee processing methods: Strip-picked, unsorted, sundried cherries; Overripe, sorted, sundried cherries; ripe, sorted, sundried (Natural) cherries; ripe, sorted, Pulped, sundried parchment; and ripe, sorted, wet fermented (Washed), sundried parchment were processed separately. The resulting green beans underwent sensory descriptive cupping, seed germination tests, and metabolite profiling using LC-HRMS. The Pulped and Washed methods produced coffees with higher sensory attributes scores, while the Overripe method was associated with the sensory `potato taste' defect. Washed coffee was characterized by smooth, fruity, cocoa notes, and was negatively correlated with rough mouthfeel, tobacco, and leather flavors. The Pulped and Washed method had significantly higher germination success after four months of storage. The processing method influenced caffeine concentration in green beans, depending on the genotype, while trigonelline levels varied significantly between genotypes but not between processing methods. The grouping of the metabolite profiles of roasted coffee and green beans was consistent with their genetic background rather than the processing method. Two metabolite marker compounds predictive of genotype in roasted coffee were putatively identified as cafamarine and likely theobromine, theophylline or paraxanthine. A metabolite feature, putatively identified as O-methylcorypalline, was a marker compound for genotype in both roasted coffee and green beans. Overall, we demonstrate that genotype plays a significant role in mediating the outcomes of different processing methods.