In the present work, the thermophilic aerobic membrane reactor technology was studied for the treatment of high strength aqueous wastes mainly containing dyes, surfactants and solvents. The thermophilic biomass resilience and the process stability under critical conditions (such as rapid rise of the mixed liquor pH, oxygen supply interruption, etc.) were also evaluated. The experimental work was carried out with the use of a pilot plant at semi-industrial scale, which was managed throughout for 14 months; the operation temperature was 49 °C and the organic loading rate was increased from 3 to 12 kgCOD m−3 d−1. Critical conditions, especially the interruption of oxygen supply, affected the pilot plant performance but did not cause a complete system break down. After the temporary reduction of process performance, also proven by the decrease in the oxygen consumption, the normal working conditions were restored. Moreover, the longer non-aerated phase involved a significant reduction (40%) of volatile suspended solids concentration in the biological reactor and the increase of 30% in foaming power; nevertheless, once the oxygen supply was reactivated, optimal conditions were rapidly restored. Therefore, the study showed the high resilience of the thermophilic biomass, which was able to recover full functionality after critical events.