The current study presents a detailed evaluation and comparison between two integrated anaerobic–aerobic systems for biological wastewater treatment under equal conditions in all aspects (wastewater characteristics, climatic conditions, reactor sizing, and even the measurement methods). The two examined systems are (i) a hybrid upflow anaerobic sludge blanket (hybrid UASB) coupled with integrated fixed-film activated sludge (IFAS) and (ii) a conventional UASB coupled with activated sludge (AS). The present comparative study aims to evaluate and assess the effect of adding carrier-filling media on the performance of the classical integrated UASB-AS. The two parallel pilot-scale systems, hybrid UASB-IFAS and UASB-AS, were installed and operated at a wastewater treatment plant. Three sets of experiments were conducted to examine the influence of the hydraulic retention time (HRT) on the consequent organic and hydraulic loads, temperature, and recirculation rate of the proposed systems. The main results showed that the two investigated systems had a comparably high efficiency for the removal of organic matters and ammonia. Moreover, a paired sample t-test indicated there was a statistically significant effect of the filling media, and the performance of the hybrid UASB-IFAS increased significantly compared with that of the UASB-AS system. An additional benefit of the filling media on the hybrid system was its high stability when changing the organic and hydraulic loads. The optimum HRT was 6 h, with a total chemical oxygen demand (TCOD) percentage removal of approximately 95% in both examined systems. Treatment of sewage under high and low temperatures indicated that increasing the temperature improved the efficiency of the overall process for both systems significantly.