Electric field (EF) processing has been suggested to be a promising technology in the valorisation of side-streams, such as whey, by enhancing the functionality of biomacromolecules. Shifting from batch to continuous processes and utilising more industry-relevant matrices are of great interest, yet studies thereof are lacking. A continuous plate–plate microsecond pulsed electric field (μsPEF) setup was optimised and whey protein concentrate (10%, w/w) was treated at 3 kV cm−1, 10 μs, 40–50 Hz. A diffuser inlet/outlet improved the process stability considerably. Average outlet temperatures between 64.1 °C and 73.2 °C were investigated and aggregate formation between 0.04 μm and 2000 μm was quantified. μsPEF-triggered particles were compared with those obtained in thermal treatments, conducted in a modular micro reaction system (MMRS) with similar temperature and residence times. A comparison of the Sauter mean diameter revealed that in the given EF process window, mainly thermal effects were responsible for aggregation shifts.