The organic compound composition of wastewater, serves as a crucial indicator for the operational performance of activated sludge processes and has a major influence on the development of filamentous bulking in activated sludge. This study focused on the impact of typical soluble and slowly-biodegradable organic compounds, investigating the pathways through which these substrates affect the occurrence of filamentous bulking in systems operated under both high- and low-oxygen conditions. Results showed that slowly-biodegradable organic compounds lead to a concentrated distribution of microorganisms within flocs, with inward growth of filamentous bacteria. Both Tween-80 and granular starch treated systems exhibited a significant increase in protein content. The glucose system, utilizing soluble substrates, exhibited a markedly higher total polysaccharide content. Microbial communities in the Tween-80 and granular starch treated systems were characterized by a higher abundance of bacteria known to enhance sludge flocculation and settling, such as Competibacter, Xanthomonadaceae and Zoogloea. These findings are of high significance for controlling the operational performance and stability of activated sludge systems, deepening our understanding and providing a novel perspective for the improvement of wastewater treatment processes.