The non-thermal effect of electromagnetic field (NEF) on the structural and thermal properties of heat-resistant globular sunflower protein isolate was investigated by exposing samples to varying power levels (70 W, defrost (DF), and 350 W). Only the lowest consecutive power modes of the electromagnetic unit were conducted to complete at least two exposure cycles (for certainty) without exceeding 45 degrees C (non-thermal processing condition). The total polar amino acid content of the treated samples decreased by 14% with NEF applications since polar amino acids were the main targets of the electromagnetic field due to absorbing that energy as kinetic energy and inducing structural changes. The DF and 350 W treatments dissipated large particles/aggregates over 5000 nm completely. The treatment with the lowest power (70 W) produced the lowest average particle size (14% decrease) while it increased after the DF and 350 W applications (34 and 16%, respectively), which indicated partial unfolding and/or reaggregation. Less ordered structures had increased alpha-helix (max with 350 W by 22%) and decreased beta-sheet contents (max with 70 W by 30%) after the NEF treatments. The tertiary structures of the samples changed significantly following the NEF treatments with a blue shift on emission maxima with different fluorescence intensities. The thermal stability of the samples was analyzed with DSC and TGA; lower peak temperature (decreased by 28%) and denaturation enthalpy (decreased by 82%) besides higher gravimetric loss (by 1.3%) were obtained for DF and 350 W, compared to the control. The NEF could be considered a promising approach for structural alteration of globular sunflower protein.