Phytoprostanes (PhytoPs) and phytofurans (PhytoFs) are plant oxylipins (isoprostane-prostaglandin-like compounds) formed by the free radical-catalyzed oxidation of α-linolenic acid (ALA, C18:3, n-3). These oxylipins have been previously described in an array of plant-based foods with similar concentrations as phenolics in some fruits and vegetables, but their occurrence in dark chocolate has not been addressed so far, neither their content nor the influence of cocoa percent and fatty acid composition on the generation of PhytoPs and PhytoFs, to establish new assays in order to boost the dietary burden of these new bioactive compounds, provided by natural plant-based foods intake. In this regard, 80 dark chocolate samples with cocoa (Theobroma cacao L.) content of up to 100% were assessed on their PhytoP and PhytoF profile. These target analytes were isolated using a dispersive liquid–liquid extraction followed by a solid-phase clean-up of the extracts, and quantified using a UHPLC coupled to a triple quadrupole-MS/MS detection system. The content of PhytoPs and PhytoFs in the array of chocolates analyzed oscillated from 2.45 to 1192.43 ng/g fw and from 144.57 to 840.19 ng/g fw, respectively. The profile of these metabolites was studied in conjunction with the fatty acid methyl esters (FAMEs) content and the percentage of cocoa; however, no relationship between PhytoPs and PhytoFs and FAMEs content nor the cocoa percentage was observed. The assessment of dark chocolates on the content of PhytoPs and PhytoFs is of great importance as there is increasing scientific evidence on their immunomodulatory and inflammatory activity, as well as their role as preventive agents against oxidative stress that could confer this food an additional interest to consumers.