Plant oxylipins (PO), including phytoprostanes (PhytoPs) and phytofurans (PhytoFs), are bioactive markers of lipid oxidation derived from alpha-linolenic acid and are recognized as early indicators of food oxidation. This study evaluated PO formation during post-harvest processing of four Colombian cocoa bean clones (FSV 41, FEC 2, FEAR 5, and FMA 7) under two conditions: controlled fermentation with starter cultures and drying (T1), and natural fermentation and drying (T2), followed by storage. PhytoPs ranged from 1.237 to 236.072 ng g-1 and PhytoFs from 0.027 to 487.35 ng g-1. Ent-16-F1t-PhytoP and Ent-9-(RS)-12-epi-ST-Delta 10-13-PhytoF were the most representative compounds. Lower PO levels under T1 were observed in FEAR 5, FEC 2, and FMA 7 clones. Fermentation was identified as a key stage in PO generation, strongly influenced by genotype, time, and postharvest conditions. This work provides a comprehensive assessment of PO evolution during post-harvest and storage, improving understanding of fatty acid oxidation in cocoa and supporting food quality improvement.