The aim of this study was to investigate the impact of a pulsed electric field (PEF) on the structural and functional properties of quinoa protein isolate (QPI). The findings revealed a significant alteration in the secondary structure of QPI following PEF treatment, converting the random coil into theβ-sheet, resulting in an improvement in structure orderliness and an enhancement of thermal stability. The PEF treatment led to a reduction in particle size, induced structural unfolding, and increased the surface hydrophobicity, resulting in a statistically significant enhancement in the solubility, foaming, and emulsifying properties of QPI . Specifically, PEF treatment at 7.5 kV/cm for 30 pulses was identified as the optimal condition for modifying QPI. This study provides a basis for the precision and range of application of pulsed electric field treatment and offers the possibility of improving the physical and chemical properties of quinoa protein.