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To substantiate and interpret the performance of the Enhanced Biological Phosphorus Removal (EBPR) processes with simultaneous nitrogen removal in five full-scale sequencing batch reactors (SBR) systems (with or without pre-anoxic/anaerobic selector) across India, conventional microscopic examinations were performed. Regular examining and cyclic behavior evaluation studies specified that these systems worked for EBPR with effectiveness depending on the wastewater quality and operational steadiness. Treatment with Neisser stain for identifying polyphosphates (poly-P) and Sudan black B stain for observing poly-β-hydroxybutyrates (PHB) granules showed that the enriched biomass of the SBR plants was very diverse concerning morphology, residing populations of traditional rod-shaped PAOs, tetrad (or Sarcina-like cells) forming organisms (submitted as TFOs instead of GAOs), diplococci-shaped cells, and staphylococci-like clustered populations (CC), including few filaments which correlate well with biochemical processes undergoing in SBR plants. SBR plants with readily biodegradable chemical oxygen demand (rbCOD) fraction in COD > 16% and rbCOD/TP ∼10–20 in Varanasi, Mumbai, and Gurgaon, respectively, have performed for >20% EBPR (∼77.8%, ∼76.6%, and ∼84.8% TP removal, respectively) as well as >85% Simultaneous Nitrification and Denitrification (SND). This study can open novel dimensions for optimization by relating microscopic observations (qualitative examination) with the processes undergoing in the plants under varied physicochemical parameters. HIGHLIGHTS Five full-scale SBR plants are analyzed for the study.; STPs at Varanasi, Mumbai, and Gurgaon achieved >75% TP removal.; Opens novel dimensions for optimization relating to microscopic studies and biochemical processes.; Strictly upholding anaerobic conditions in the anaerobic zone enhances EBPR.; The biomass of the SBR plants was very diverse.;