The present study investigated the disregarded impact of microbial community composition, diversity and abundance of the starter biomass on lab-scale bioreactor performance, steady-state long time operation, biodegradation outcome and microbial kinetics. Standard lab-scale experiments are usually initiated with inoculum taken from wastewater treatment plants (WWTPs) without considering microbial community composition. Two identical sequencing batch bioreactors (SBR-1, SBR-2) were operated with inocula obtained from two domestic WWTPs to assess the role of inoculum composition on reactor performance and treatment efficacy. Filamentous microorganisms were dominated in SBR-1 (SVI: 265 mL/g), whereas their supremacy was diminished in SBR-2 (SVI: 160 mL/g). Next generation sequencing analyses verified high abundance of Candidatus Microthrix (14%) and Kouleothrix spp. (3%) in SBR-1. Although Chloroflexi C10-SB1A metagenome accounted for 16% of WWTP-2 community, SBR-2 was operated at steady-state for longer period without deterioration. Statistical indicators based on molecular studies showed that WWTP-2 has higher diversity than WWTP-1. Higher biodiversity in WWTP-2 community supported the stable process performance. Modelling studies denoted an increase in half saturation coefficients (K-s) in filamentous microorganisms dominated reactor. The results of this study provide insight on how the filamentous organisms typically found in WWTPs become a fundamental constituent during the bioreactor operation.