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Pulsed electric fields (PEF) technology has been used as a sustainable method for extracting antioxidant bioactive compounds from different food matrices. In the present study, the optimal conditions of PEF extraction for mushrooms (2.5 kV/cm, 50 kJ/kg, 6 h) were applied to Lentinula edodes , Agaricus brunnescens , and Pleurotus ostreatus to evaluate the total antioxidant capacity of the extracts, followed by the Triple TOF-LC-MS-MS analysis of the phenolic profile compared to A. bisporus by high-performance liquid chromatography coupled to mass spectrophotometry. In addition, the microporation effect of the technology on the mushroom surface was evaluated using scanning electron microscopy. A comparison was made with a maceration extraction (aqueous stirring for 6 h). The results showed that PEF-assisted extraction enhanced the recovery of antioxidant compounds such as 3,5-dicaffeoylquinic and cinnamic acid with contents up to 236.85 µg/100 g dry weight and 2043.26 µg/100 g dry weight from A. bisporus , respectively. However, mixed results were obtained for certain phenolic compounds, including vanillic acid from L. edodes , ellagic acid from P. ostreatus , and thymol from all mushrooms. These results indicate that the application of PEF technology is effective for the extraction of antioxidant compounds in fungal matrices by creating micropores in cell membranes that allow great recovery in matrices with high content of bioactive compounds.