Phytoprostanes (PhytoPs) and phytofurans (PhytoFs) are isoprostanoids that result from the peroxidation of α-linolenic acid and are biomarkers of oxidative stress in plants and humans. These compounds exhibit several interesting biological activities (e.g. neuroprotection and anti-inflammatory activities). The aim of this research was to add value to coffee pulp (CP), cocoa husk (CH) and cocoa pod husk (CPH) by identifying and quantifying PhytoPs and PhytoFs by liquid chromatography-tandem mass spectrometry. The contents of PhytoPs and PhytoFs in CP, CH, and CPH were, respectively, 654.6, 474.3 and 179.9, and 543.2, 278.0 and 393.8 ng per g dry weight (dw). The main PhytoP found in CP (171.37 ng per g dw) and CPH (37.12 ng per g dw) was 9-epi-9-F1t-PhytoP, while ent-9-L1t-PhytoP was the most abundant in CH (109.78 ng per g dw). The main PhytoF found in all sources was ent-16(RS)-13-epi-ST-Δ14-9-PhytoF, at 196.56, 126.22, and 207.57 ng per g dw in CP, CH, and CPH, respectively. We provide the first complete profile of PhytoPs and PhytoFs for these agro-residues, which could be used in the functional food industry for enriching food or as nutritional supplements.