Whey proteins are being integrated as high-value food product ingredients due to their versatile and tunable techno-functionality. To meet high food quality and clean label expectations by consumers, electric field (EF) technologies have been proposed to open new frontiers in this field. Despite a variety of studies, it remains ambiguous which EF parameters are crucial to achieving targeted whey protein modifications. Reconstituted liquid whey protein concentrate (WPCL) and filtered, non-heat-treated liquid whey (WPL_filt) at low protein dry weight concentrations (0.4% wt/wt) were exposed to microsecond pulsed electric field (μsPEF) treatments at EF intensities between 1.25 and 12.5 kV/cm, pulse repetition frequencies between 0.38 and 85 Hz, and pulse lengths set to 10 or 100 μs. Protein aggregations were quantified spectroscopically. We report here that aggregates formed at lower temperatures for μsPEF compared with purely thermal treatments in identical treatment geometries at similar time-temperature profiles. We suggest that the observed increase in absorbance is linked to protein migration, the isoelectric point, local deprotonation phenomena of thiol groups, and cation precipitation. The μsPEF treatment time, which is dependent on the pulse repetition frequency, pulse length, and time of process, is the main driver of the increase in absorbance. High EF intensities balanced with shorter pulse repetition frequencies to ensure similar energy inputs resulted in no aggregate formation. For WPL_filt, 12.5 kV/cm, 10 μs, 0.38 Hz (620 ± 96 kJ/kg; ± standard deviation) did not result in an increase in absorbance, whereas 1.25 kV/cm, 10 μs, 50 Hz (634 ± 57 kJ/kg) with similar time-temperature profiles increased the absorbance at a wavelength of 380 nm by a factor of 8.2 ± 1.7 compared with untreated WPL_filt. In conclusion, the treatment time seems to dominate over high EF intensities at similar energy inputs for aggregate formation and increase in absorbance.