Consumption of foods rich in anti-nutritional factors (ANFs) can lead to inadequate absorption of vitamins and minerals. Pulsed electric field (PEF) treatment is a non-thermal food processing technology that uses short bursts of high voltage electric fields to induce structural modifications in biomolecules, including proteins, through electrochemical reactions and polarization of structural moieties. PEF offers potential benefits in enhancing the nutritional quality of food products by altering the structure and function of ANFs. However, the effects of PEF on ANFs in food have not been well established. Additionally, PEF-treated samples may undergo protein structural orientation modification due to electroporation and free radical species, potentially unfolding the native structure and influencing protein digestibility. Moreover, by increasing the mass transfer rate, electroporation can enhance the extraction of the initially trapped fractions into the solvent medium, which may include target compounds that affect protein functionality and digestibility. However, the protein digestibility of PEF-treated food products is yet to be thoroughly explored. Therefore, this review objectively investigates the possible mechanisms involved and the effectiveness of PEF in reducing different ANFs and modifying plant protein digestibility. This review also provides in-depth information about the possible applications of PEF-treated food items in the food industry.