The aim of the study was to compare and select the most efficient green extraction technique (ultrasound-assisted extraction (UAE), deep eutectic solvent microwave-assisted extraction (DES/MAE), high voltage electric discharge extraction (HVED), supercritical CO2 extraction (SC-CO2) and subcritical water extraction (SWE) of bioactive compounds from food industry by-product ꟷ cocoa shell. The following compounds were identified and quantified: methylxanthines (theobromine, caffeine and theophylline), phenolic compounds (gallic acid, epicatechin, epigalocatechin, catechin, chlorogenic acid, caffeic acid and vanillin) and hydroxymethylfurfural in different concentrations depending on the selected extraction technique. The amount of compounds was determined by using high performance liquid chromatography (HPLC) with diode array detector. The influence of different extraction parameters was examined as follows: UAE ꟷ temperature, time, liquid/solid ratio, ultrasound power; DES/MAE ꟷ type of eutectic solvent, water content in solvent, temperature, time; HVED ꟷ liquid/solid ratio, frequency, time; SC-CO2 ꟷ pressure, temperature, time, and SWE ꟷ temperature, time, liquid/solid ratio. The optimization of each individual extraction technique was performed by response surface methodology (RSM). The antioxidant activity of the obtained extracts as well as the total phenolic content were determined as well. In SC-CO2 extracts, the fatty acid composition was determined by gas chromatography with flame ionization detector as follows: oleic, palmitic, stearic, linoleic and palmitoleic acid. SWE proved to be the most suitable for the isolation of theobromine, catechin and epicatechin, as well as for the highest total phenolic content and antioxidant activity, while SC-CO2 proved to be the most suitable solvent for the extraction of caffeine. Hydroxymethylfurfural and theophylline were presented only in extracts obtained by SWE performed at higher temperature (220 °C). UAE proved to be the most suitable for the extraction of gallic acid while DES/MAE was most suitable for extraction of caffeic acid. Chlorogenic acid as well as epigalocatechin and vanillin were under the limit of detection.