High-valued nutritional and therapeutic proteins are often recovered from dilute wastewater streams by electroultrafiltration. In protein electroultrafiltration, use of pulsating d.c field has long been confirmed to be substantially advantageous relative to its equivalent constant d.c applications. However, the root cause behind this enhanced performance remained unexplored over years. In this article, we have presented a first-of-its-kind explanation from the perspective of fatigue rupture in the fouling protein layer. BSA-water solution was used as the synthetic wastewater feedstock. We have constructed the fatigue stress-life plot of the visually inaccessible protein layer only from the field-induced transient flux regeneration profile after conducting the initial cross-flow experiment without any electric field. Maximum flux regeneration (205 %) was achieved at moderate field strength (10,000 V.m−1) and low frequency (10 Hz). Corresponding regeneration in constant d.c EUF was limited to 119 % only. The study provides an insight to the complex interaction between the protein and the pulsating electric field and is expected to outline the appropriate protocol for the effective recovery of proteins from wastewater. © 2021 Elsevier Ltd