The activated sludge process suffers from rapid load changes of ammonium (NH4), which may result in process failure during wastewater treatment. In this study, the response of activated sludge properties in terms of microfauna composition and sludge volume index (SVI5 and SVI30) on short-term increase of NH4 concentration (from 55 mg/l to 105 mg/l) was evaluated in batch scale reactors over 72 h. The results show that the first-step nitrification (NH4 transformation to nitrite (NO2)) was inhibited after 24 h, whereas the second-step nitrification (NO2 transformation to nitrate (NO3)) was not significantly affected. Sludge volume indices (sedimentation ability characteristics) SVI5 and SVI30 in the reactor with NH4–N shock concentration increased, whereas microfauna diversity decreased (Shannon–Weaver index decreased from 2.12 at 48 h to 1.23 at 72 h) leading to dominance of stalked ciliate Epistylis sp. Notable changes in inorganic carbon concentration (IC) were observed, indicating that rapid decrease of IC concentration leads to nitrification inhibition and challenges the overall process recovery. To conclude, short-term exposure of about two times higher concentration of NH4 caused significant changes in activated sludge properties by inhibiting NH4-oxidizing bacteria, reducing sludge microfauna diversity and deteriorating sludge sedimentation ability.