The fava bean protein isolate (FBPI) holds promise as a sustainable plant-based protein ingredient. However, native FBPIs exhibit limited functionality, including unsuitable emulsifying activities and a low solubility at a neutral pH, restricting their applications. This study is focused on the effect of ultrasonication (US) and pulsed electric fields (PEF) on modulating the techno-functional properties of FBPIs. Native FBPIs were treated with US at amplitudes of 60–90% for 30 min in 0.5 s on-and-off cycles and with PEF at an electric field intensity of 1.5 kV/cm with 1000–4000 pulses of 20 μs pulse widths. US caused a reduction in the size and charge of the FBPIs more prominently than the PEF. Protein characterization by means of SDS-PAGE illustrated that US and PEF caused severe-to-moderate changes in the molecular weight of the FBPIs. In addition, a spectroscopic analysis using Fourier-transform infrared (FTIR) and circular dichroism (CD) revealed that US and the PEF induced conformational changes through partial unfolding and secondary structure remodeling from an α-helix to a β-sheet. Crystallographic and calorimetric determinations indicated decreased crystallinity and lowered thermal transition temperatures of the US- and PEF-modified FBPIs. Overall, non-thermal processing provided an effective strategy for upgrading FBPIs’ functionality, with implications for developing competitive plant-based protein alternatives.