Coffee pulp (CP), cocoa husk {CH) and cocoa pod husk (CPH), are the main by-products (CP, CH) and co-product (CPH) derived from green coffee and cocoa transformation. These wastes represent a non-expensive source of interesting biomolecules. Phytoprostanes {PhytoPs) derived from peroxidation of a-linolenic acid (C18:3 n-3, ALA) are biomarkers of oxidative stress in plants and humans and possess biological properties. Under high oxygen tension, phytofurans (PhytoFs) derived from ALA, were recently discovered in seeds, nuts, oils, and melon's leaves. There is a growing interest in the profile of these compounds in plant foods and their response to cultural, postharvest, and/or environmental conditions. The goal of this work was to identify and to quantify the PhytoPs and PhytoFs in the vegetal matrices, by micro-Le coupled to a QTRAP detector method. The content of PhytoPs and PhytoFs, found, were, respectively, of 663 and 543.1 {from CP), 438.8 and 278 {from CH), and, 149.8 and 393.7 {from CPH) ng/g dry basis {d.b.). 9-epi-9-Flt-PhytoP was the main PhytoP found in CP {171.4 ng/g d.b.) and CPH {37.1 ng/g d.b.), while ent-9-Llt-PhytoP was the main PhytoP in CH {109.8 ng/g d.b.). Additionally, ent-16(RS)-13-epi-ST-ti14-9-PhytoF was the main PhytoF found in our samples {196.5, 126.2, and 207.6 ng/g d.b., from CP, CH, and CPH, respectively). This is the first time that a complete profile of these oxygenated lipids is realized in coffee and cocoa, showing the potential of plant biomass by- and co-products to be used as a source of these biomolecules.